From 4af4fd392152893ede4509fc14c0b0268e95c533 Mon Sep 17 00:00:00 2001 From: Emma Rand Date: Fri, 6 Oct 2023 14:47:49 +0100 Subject: [PATCH] update omics workshop 1 and associated overviews of week --- about.qmd | 5 - login-key-nerc-metagenomics-instance-emma.pem | 27 ------ omics/omics.qmd | 25 ++--- omics/week-3/data-processed/s30_filtered.csv | 95 +++++++++++++++++++ .../s30_summary_gene_filtered.csv | 95 +++++++++++++++++++ .../data-processed/s30_summary_samp.csv | 7 ++ omics/week-3/overview.qmd | 19 ++-- omics/week-3/study_after_workshop.qmd | 2 + omics/week-3/study_before_workshop.qmd | 32 ++++--- omics/week-3/workshop.qmd | 65 ++++++++----- update-notes.txt | 14 +++ 11 files changed, 293 insertions(+), 93 deletions(-) delete mode 100644 about.qmd delete mode 100644 login-key-nerc-metagenomics-instance-emma.pem create mode 100644 omics/week-3/data-processed/s30_summary_samp.csv diff --git a/about.qmd b/about.qmd deleted file mode 100644 index 07c5e7f..0000000 --- a/about.qmd +++ /dev/null @@ -1,5 +0,0 @@ ---- -title: "About" ---- - -About this site diff --git a/login-key-nerc-metagenomics-instance-emma.pem b/login-key-nerc-metagenomics-instance-emma.pem deleted file mode 100644 index cee590a..0000000 --- a/login-key-nerc-metagenomics-instance-emma.pem +++ /dev/null @@ -1,27 +0,0 @@ ------BEGIN RSA PRIVATE KEY----- -MIIEowIBAAKCAQEA3dMPPWPtWdvAkWQZfVRe19tHsgkCqpZQrl37bP3vXaoJnxHN -BIxAYhX5RKT0QjbDOqHMvdRI5i3jRYuUhA4aMKD914T93GYS8b4NdDbhCqCAetuc -Rkqc5vhA5BkJDgDRCjGenwzeeFhOlGGMxIeKqwF1eMf4yNz/JKWWghNrwKxIGKAy -i42wOYoQid/k3WpNuPxWGPrl6X/vYLSo/97EGnWMjW0ytS4yw8vFwh023+bIq9ZT -VzFwN5kaCQReSt7U2PvirD1AGOyP3TRW9/vMTug2ZzH7pgwMRaJXog65X94XNFIZ -9zIqp7CJTq35BPq1NM447vGiOC9Owdj3y2NKwQIDAQABAoIBAAOfJIqODRwAeH5n -MftX20yO6fbAKuj6F0shga9f3f6bfhi4w64lVA/F6BH014AVQM6+QYd/5cjMSv+h -rcUSLd9JYZuZMkPc7sY/ohyZoMb5o99doomLQlCLERQoTHuMC92svbg/D4rLdkz5 -4sB6rgrotTBJo4g0A35nrbNl+cZlgefBh0640whWWhgInUykC50WC1qmohSC6wB2 -+uGhiSYBEdSSZYX/LEmK1BlOy31q4U8xtwfsBC41jmzI2R+r68nmg/MRqTQPbrwd -QulehMjEf53mRUEBpqoYQWwudxXZERpGS3VV/iQ+Q+b8CdMz8Et7Hm6771ysH4UN -WB5H6TkCgYEA77L01WBQtlT1ex4V2obChbSx4XkpNmGOFDYXogiRji3Nfu3jZqrJ -dq8CQ6Dqlb8BkXbmcbslTGSn0MqcUjegabil9bJnsaZVmBk+qBANp3KID2YCPtQX -i8BkBpDtIO9PDDeRQZtvRlJnKiqc7zdjcuNMuc0EhqlyA7Ds5L6NQfcCgYEA7Ojq -RamIKPynJGbVrx9OPXVMviXNrsdY2eDtkosPTAu1Ay6Ojy0oYAmDu4SDTkvfTLjC -XpYOB4nLVR/0v95bvIPKt3uaKB1DhI3ju6y7YsI6vK5un83pGL7sIRykZxQrw9kC -dtT0TYw3odUgoqCq/3dyrwSmRBXNCbVSMcOeKwcCgYEAjLEKmg+tcEgPylMPWrPM -i3RTEFfwg7XhEiXp2zaSUNS7kGwLFKDcHWh9uLpD1t9FCV+zxT+mld9izN+Pv4Zd -BpDWAI/V42URSnRO3ZCGoylLiVZDrSMKKwIi8+Ou+6zbRf17qfmU577IROy8LoDh -Q3b8+vXGWVAt1tLLSTw7Z2MCgYBeFNkENSEXdc5CjHwLgZkmmvCRCp417ICCdeqi -qYq3nmaSDukaPsqr6NthmmwyqbrR0wWNXnXP1I7lDT26/Gjd4lCcsP81MvnfKCHq -I9x+ibedun/AApuw8hD/zUoUjVQcAJAT9NnX+fkV0XeWXcvKi/sFOgl1PFsiodk0 -XgTv/QKBgBbC9dq+9Y53U2cVuP5EWphujUkojUi4rmV9FKREb7V7YfoADnnIh4yM -oorA1XRNWlMlecLihKXv9tYAC6XQwvOuvTlIDEQDS1rsmyUjF9LaAADJu9DJWFWd -qQ3IexFMyB4nhKu5ZZ7HHquf/L0ZSlGVEjF0zD7iUX1FzboNfiA6 ------END RSA PRIVATE KEY----- diff --git a/omics/omics.qmd b/omics/omics.qmd index fe120b2..5d4af92 100644 --- a/omics/omics.qmd +++ b/omics/omics.qmd @@ -8,30 +8,15 @@ toc-location: right ## Omics 1: Hello data! -before -- sequence data fundamentals -- where have the data come from -- processing so far -- why log2 -- overarching aims - -workshop -- set up a project and create the organisation -- meta data -- open in understanding the data numbers of variables, organisation -- importing -- exploring, what kind of values are they, how many missing -- qc plots -- removing the useless, writing to files +This week you will meet your data. The independent study will concisely cover how these data were generated and how they have been processed before being given to you. There will also be an overview of the analysis we will carry out over three workshops. +In the workshop, you will learn what steps to take to get a good understanding of ’omics data before you consider any statistical analysis. This is an often overlooked, but very valuable and informative, part of any data pipeline. It gives you the deep understanding of the data structures and values that you will need to code and trouble-shoot code, allows you to spot failed or problematic samples and informs your decisions on quality control. -after -- document what you have done -- format your figures ## Omics 2: Statisitcal Analysis before + - which genes matter: expression, DE - goal of DE - how does DE work @@ -46,12 +31,14 @@ workshop - writing to files after + - document what you have done - repeat on another comparison ## Omics 3: Visualising and Interpreting before + - recap what we have - volcano plot described - GO terms @@ -59,6 +46,7 @@ before workshop + - open project import the data - revise! - volcano plot @@ -66,5 +54,6 @@ workshop - annotating with go terms after + - document what you have done - repeat on another comparison diff --git a/omics/week-3/data-processed/s30_filtered.csv b/omics/week-3/data-processed/s30_filtered.csv index 9abb2cb..6362079 100644 --- a/omics/week-3/data-processed/s30_filtered.csv +++ b/omics/week-3/data-processed/s30_filtered.csv @@ -44,6 +44,7 @@ XB-GENE-1001088,268,261,468,358,267,253 XB-GENE-1001113,139,154,222,149,193,151 XB-GENE-1001131,56,36,64,29,55,31 XB-GENE-1001158,155,221,273,293,213,236 +XB-GENE-1001182,0,0,10,2,2,9 XB-GENE-1001202,211,116,186,251,157,113 XB-GENE-1001213,106,131,196,136,107,147 XB-GENE-1001247,45,52,72,64,60,30 @@ -298,6 +299,7 @@ XB-GENE-1007210,81,118,114,129,133,86 XB-GENE-1007229,97,136,223,180,169,193 XB-GENE-1007241,198,263,254,209,297,184 XB-GENE-1007252,244,245,290,298,246,164 +XB-GENE-1007263,1,0,2,0,1,21 XB-GENE-1007284,89,89,104,84,103,71 XB-GENE-1007301,292,272,266,221,297,96 XB-GENE-1007318,389,367,478,435,375,294 @@ -435,6 +437,7 @@ XB-GENE-1010862,129,217,326,245,250,255 XB-GENE-1010880,47,61,83,84,70,67 XB-GENE-1010935,53,49,93,51,52,50 XB-GENE-1010966,27,34,47,35,30,29 +XB-GENE-1010995,0,0,32,24,45,46 XB-GENE-1011022,23,28,35,41,28,32 XB-GENE-1011062,481,458,658,525,508,377 XB-GENE-1011071,30,36,62,37,39,47 @@ -722,6 +725,7 @@ XB-GENE-1018177,22,23,43,28,30,27 XB-GENE-1018199,228,241,287,267,264,204 XB-GENE-1018219,9574,9068,9451,12168,11485,4662 XB-GENE-1018237,798,908,745,738,852,377 +XB-GENE-1018260,0,0,0,10,2,16 XB-GENE-1018301,459,391,456,702,367,359 XB-GENE-1018369,13,15,26,23,22,14 XB-GENE-1018436,9,9,9,20,5,14 @@ -869,6 +873,7 @@ XB-GENE-17330101,34,11,18,22,17,14 XB-GENE-17330102,168,189,267,166,189,150 XB-GENE-17330103,85,70,102,91,101,65 XB-GENE-17330114,21,21,29,46,33,19 +XB-GENE-17330117,0,0,0,13,4,17 XB-GENE-17330129,268,327,411,350,353,283 XB-GENE-17330152,403,374,446,438,409,275 XB-GENE-17330155,63,51,53,53,52,35 @@ -1047,6 +1052,7 @@ XB-GENE-17332140,449,579,842,627,619,505 XB-GENE-17332144,78,98,139,91,99,72 XB-GENE-17332152,97,114,136,106,105,94 XB-GENE-17332177,51,39,55,66,48,26 +XB-GENE-17332184,0,0,0,6,19,6 XB-GENE-17332198,101,125,178,162,166,171 XB-GENE-17332215,50,72,70,64,56,32 XB-GENE-17332218,26,31,17,17,14,14 @@ -1113,6 +1119,7 @@ XB-GENE-17332824,846,805,1082,910,942,704 XB-GENE-17332831,25,31,32,27,31,20 XB-GENE-17332842,10,6,21,10,11,12 XB-GENE-17332853,143,90,209,133,76,96 +XB-GENE-17332870,0,0,2,3,2,16 XB-GENE-17332882,150,114,145,173,103,90 XB-GENE-17332887,776,717,861,765,769,501 XB-GENE-17332896,81,76,33,89,111,29 @@ -1357,6 +1364,7 @@ XB-GENE-17335595,31,44,68,45,58,42 XB-GENE-17335605,185,224,351,212,234,211 XB-GENE-17335630,225,292,253,258,346,183 XB-GENE-17335632,49,50,43,49,42,47 +XB-GENE-17335658,0,5,0,62,12,16 XB-GENE-17335663,38,79,139,65,130,117 XB-GENE-17335669,15,24,22,24,20,15 XB-GENE-17335673,323,356,603,337,335,318 @@ -1383,6 +1391,7 @@ XB-GENE-17335896,93,114,84,93,130,52 XB-GENE-17335907,138,126,167,169,132,82 XB-GENE-17335927,201,263,316,352,290,277 XB-GENE-17335932,475,711,768,548,732,361 +XB-GENE-17335943,0,45,0,17,67,0 XB-GENE-17335950,10,9,37,11,19,15 XB-GENE-17335969,849,916,1249,989,1022,733 XB-GENE-17335972,0,1,9,43,5,24 @@ -1539,6 +1548,7 @@ XB-GENE-17337633,1957,1829,3508,2439,2603,1527 XB-GENE-17337640,488,640,945,773,706,736 XB-GENE-17337654,163,202,235,201,203,124 XB-GENE-17337674,88,102,113,115,113,117 +XB-GENE-17337706,0,0,4,83,26,91 XB-GENE-17337728,66,64,92,66,78,48 XB-GENE-17337733,7,4,8,8,13,8 XB-GENE-17337768,135,135,197,168,141,163 @@ -1593,6 +1603,7 @@ XB-GENE-17338313,234,434,589,458,464,362 XB-GENE-17338323,57,61,89,60,76,41 XB-GENE-17338332,65,69,105,64,58,38 XB-GENE-17338334,18,16,28,35,18,15 +XB-GENE-17338339,1,0,0,65,15,33 XB-GENE-17338353,4,1,14,2,5,4 XB-GENE-17338400,9,7,18,9,11,8 XB-GENE-17338417,1,14,3,7,5,7 @@ -1910,6 +1921,7 @@ XB-GENE-17341811,67,77,9,54,109,6 XB-GENE-17341812,800,942,2049,1012,1429,1255 XB-GENE-17341844,10,7,15,5,10,3 XB-GENE-17341853,8,9,44,18,12,17 +XB-GENE-17341857,0,2,10,0,7,3 XB-GENE-17341884,193,214,201,226,222,178 XB-GENE-17341887,260,239,407,425,256,252 XB-GENE-17341908,76,77,132,78,68,83 @@ -1956,6 +1968,7 @@ XB-GENE-17342252,28,27,58,48,51,35 XB-GENE-17342256,1283,1536,3000,1612,1465,1685 XB-GENE-17342268,48,29,64,54,28,31 XB-GENE-17342272,78,72,87,93,92,62 +XB-GENE-17342281,0,0,0,42,10,35 XB-GENE-17342282,12,6,18,9,9,14 XB-GENE-17342291,6,4,8,8,10,16 XB-GENE-17342298,72,72,98,89,60,50 @@ -2053,6 +2066,7 @@ XB-GENE-17343351,19,11,20,14,10,13 XB-GENE-17343352,29,34,60,39,50,39 XB-GENE-17343357,9,9,13,13,6,8 XB-GENE-17343367,77,70,113,86,86,74 +XB-GENE-17343376,1,2,28,0,0,1 XB-GENE-17343377,1349,949,1512,1309,1331,615 XB-GENE-17343382,28,25,31,32,27,12 XB-GENE-17343389,207,176,219,195,218,140 @@ -2072,6 +2086,7 @@ XB-GENE-17343498,64,59,73,83,58,61 XB-GENE-17343505,75,114,153,112,115,79 XB-GENE-17343511,20,27,44,14,23,23 XB-GENE-17343529,213,155,421,240,220,234 +XB-GENE-17343537,0,0,8,0,1,12 XB-GENE-17343549,9,15,42,48,24,53 XB-GENE-17343550,232,222,309,217,240,141 XB-GENE-17343582,59,18,45,57,35,28 @@ -2322,12 +2337,14 @@ XB-GENE-17346446,113,114,159,116,111,101 XB-GENE-17346458,194,165,245,219,116,157 XB-GENE-17346466,72,51,93,73,71,54 XB-GENE-17346492,2072,1937,2384,2482,2401,1591 +XB-GENE-17346494,9,0,9,0,4,7 XB-GENE-17346496,16,16,89,19,17,19 XB-GENE-17346504,28,23,54,31,25,30 XB-GENE-17346514,10,11,23,19,6,13 XB-GENE-17346530,24,28,32,46,44,40 XB-GENE-17346559,59,49,73,47,37,41 XB-GENE-17346563,358,381,441,376,442,253 +XB-GENE-17346564,1,0,34,0,0,6 XB-GENE-17346573,15,2,27,9,3,20 XB-GENE-17346577,164,198,307,207,237,184 XB-GENE-17346583,22,12,9,19,16,6 @@ -2378,6 +2395,7 @@ XB-GENE-18006009,23,23,40,28,21,17 XB-GENE-18006014,27,82,90,38,109,62 XB-GENE-18006546,14,15,12,7,13,21 XB-GENE-18034123,2,1,11,5,3,6 +XB-GENE-22041698,14,16,0,20,17,0 XB-GENE-22041729,30,25,31,74,30,36 XB-GENE-22041745,1053,1009,1152,1044,1129,679 XB-GENE-22060522,40,88,212,44,99,80 @@ -2480,6 +2498,7 @@ XB-GENE-480490,7,5,40,6,9,20 XB-GENE-480548,12,9,3,9,9,15 XB-GENE-480612,5,14,57,9,6,33 XB-GENE-480674,631,600,834,996,749,701 +XB-GENE-480721,0,1,0,34,2,5 XB-GENE-480822,301,342,297,361,359,208 XB-GENE-480859,167,170,279,203,174,140 XB-GENE-481129,3032,2765,2394,3355,3185,1934 @@ -2508,6 +2527,7 @@ XB-GENE-482706,132,108,229,173,129,152 XB-GENE-482725,35,52,69,56,44,69 XB-GENE-482744,0,7,5,31,6,48 XB-GENE-482754,91,195,237,233,207,206 +XB-GENE-482791,0,0,1,29,10,28 XB-GENE-482845,26,30,30,53,43,19 XB-GENE-482980,432,480,662,653,546,489 XB-GENE-483062,291,224,343,211,269,188 @@ -2542,7 +2562,9 @@ XB-GENE-485020,66,72,93,67,79,71 XB-GENE-485039,8,4,11,10,9,6 XB-GENE-485077,10,17,21,19,18,8 XB-GENE-485151,778,971,311,1054,1230,310 +XB-GENE-485208,0,0,0,73,17,56 XB-GENE-485224,287,307,307,186,287,95 +XB-GENE-485256,0,0,4,0,3,15 XB-GENE-485265,10,10,5,0,5,4 XB-GENE-485341,73,72,135,85,106,95 XB-GENE-485445,9,40,38,11,35,4 @@ -2550,15 +2572,19 @@ XB-GENE-485471,717,878,612,758,794,448 XB-GENE-485511,58,70,111,72,80,89 XB-GENE-485647,695,667,976,788,675,633 XB-GENE-485786,258,252,306,186,210,153 +XB-GENE-485796,0,0,0,51,10,44 XB-GENE-485811,41,29,98,48,47,64 XB-GENE-485877,376,278,463,515,323,240 XB-GENE-485979,0,13,43,4,16,11 XB-GENE-486018,596,851,466,647,857,397 XB-GENE-486365,454,457,698,507,570,461 XB-GENE-486580,1798,1923,1829,2096,2061,1024 +XB-GENE-486805,1,0,13,5,0,12 XB-GENE-486869,146,189,190,160,205,127 XB-GENE-486879,629,578,746,834,696,603 +XB-GENE-486919,0,0,0,108,18,80 XB-GENE-486929,128,136,169,174,122,159 +XB-GENE-487006,0,0,3,10,0,14 XB-GENE-487128,881,745,989,999,935,674 XB-GENE-487204,4215,3831,4747,4110,3802,2781 XB-GENE-487224,14,21,23,33,22,21 @@ -3018,11 +3044,13 @@ XB-GENE-5798587,12,9,8,12,7,5 XB-GENE-5798608,49,38,80,55,40,44 XB-GENE-5798738,866,1183,1470,1221,1254,1044 XB-GENE-5798775,4,3,9,3,3,4 +XB-GENE-5799188,0,0,1,62,24,31 XB-GENE-5799220,54,47,178,63,105,64 XB-GENE-5799265,209,216,357,244,260,168 XB-GENE-5799513,420,464,670,386,583,407 XB-GENE-5799572,424,432,388,398,437,252 XB-GENE-5799612,141,180,270,205,195,155 +XB-GENE-5799717,0,6,12,5,0,6 XB-GENE-5799848,105,153,291,128,150,193 XB-GENE-5800096,358,451,428,606,525,415 XB-GENE-5800178,31,22,76,44,26,21 @@ -3529,6 +3557,7 @@ XB-GENE-5887526,23,28,47,25,40,36 XB-GENE-5887592,80,66,122,78,98,73 XB-GENE-5887684,231,354,389,347,403,310 XB-GENE-5887850,195,187,376,248,257,227 +XB-GENE-5887902,0,0,2,77,24,55 XB-GENE-5888021,358,285,676,359,354,344 XB-GENE-5888602,151,148,218,175,135,117 XB-GENE-5888863,14,16,22,20,39,26 @@ -3616,6 +3645,7 @@ XB-GENE-5901000,83,69,95,83,74,49 XB-GENE-5901117,40,35,59,47,34,49 XB-GENE-5901616,86,83,108,99,108,60 XB-GENE-5901736,185,282,297,270,263,215 +XB-GENE-5902157,5,0,0,34,0,3 XB-GENE-5902240,48,29,60,45,41,32 XB-GENE-5902305,22,20,20,22,27,11 XB-GENE-5902323,164,163,272,185,216,163 @@ -3643,6 +3673,7 @@ XB-GENE-5905929,2,7,26,8,9,14 XB-GENE-5906854,635,783,862,963,768,641 XB-GENE-5907046,144,223,164,186,229,91 XB-GENE-5907126,54,51,86,88,70,78 +XB-GENE-5907181,2,0,24,0,1,0 XB-GENE-5907524,131,144,166,160,169,126 XB-GENE-5907787,98,74,160,121,85,80 XB-GENE-5907977,176,194,447,229,230,237 @@ -3652,6 +3683,7 @@ XB-GENE-5909030,109,131,187,147,169,123 XB-GENE-5909112,4,8,24,12,10,14 XB-GENE-5909161,25,37,55,29,32,45 XB-GENE-5909194,23,25,59,26,20,18 +XB-GENE-5909221,10,4,0,5,6,0 XB-GENE-5909289,72,86,82,77,116,45 XB-GENE-5909354,653,670,1293,800,836,636 XB-GENE-5909461,39,18,73,68,36,59 @@ -3688,6 +3720,7 @@ XB-GENE-5915054,91,136,139,88,114,85 XB-GENE-5915333,3057,3097,4980,3285,3456,2777 XB-GENE-5915552,152,182,250,212,224,222 XB-GENE-5915587,24,21,38,21,21,19 +XB-GENE-5915744,0,0,34,2,2,0 XB-GENE-5915775,13,9,14,4,9,11 XB-GENE-5915878,1722,1877,2311,1647,1975,1304 XB-GENE-5915936,73,101,125,88,120,74 @@ -3715,6 +3748,7 @@ XB-GENE-5918360,62,78,108,93,79,63 XB-GENE-5918421,67,50,80,49,39,25 XB-GENE-5918483,4,21,7,12,9,11 XB-GENE-5918613,398,295,799,350,351,393 +XB-GENE-5918635,0,0,15,0,2,6 XB-GENE-5918699,63,65,100,80,89,66 XB-GENE-5918844,85,119,167,120,123,96 XB-GENE-5918898,69,139,176,151,159,156 @@ -3965,6 +3999,7 @@ XB-GENE-5963159,181,296,232,225,316,170 XB-GENE-5963207,105,101,118,112,110,62 XB-GENE-5963305,12,11,26,10,10,7 XB-GENE-5964950,58,68,54,145,118,87 +XB-GENE-5965003,0,2,18,1,0,10 XB-GENE-5965500,381,439,565,476,500,381 XB-GENE-5966552,6,6,13,13,13,5 XB-GENE-5966967,352,348,470,425,346,270 @@ -3974,6 +4009,7 @@ XB-GENE-5967274,39,26,69,37,34,41 XB-GENE-5967430,112,108,138,120,117,82 XB-GENE-5969042,65,110,161,89,123,79 XB-GENE-5969298,2,2,8,6,2,3 +XB-GENE-5970069,0,0,22,0,2,10 XB-GENE-5970490,54,54,102,64,72,60 XB-GENE-5970708,197,181,335,237,249,178 XB-GENE-5970736,135,108,123,117,110,55 @@ -4357,6 +4393,7 @@ XB-GENE-6251329,271,347,463,395,376,271 XB-GENE-6251426,121,77,79,113,82,41 XB-GENE-6251435,239,269,416,278,299,185 XB-GENE-6251439,270,314,479,375,351,328 +XB-GENE-6251441,0,1,0,20,2,30 XB-GENE-6251449,45,64,67,72,53,56 XB-GENE-6251452,30,25,38,36,49,41 XB-GENE-6251453,179,139,278,214,174,205 @@ -4424,6 +4461,7 @@ XB-GENE-6251591,1,0,1,51,13,80 XB-GENE-6251594,137,166,175,150,136,85 XB-GENE-6251601,31,27,45,38,28,34 XB-GENE-6251606,4,1,11,3,6,8 +XB-GENE-6251607,23,0,3,12,0,1 XB-GENE-6251608,7,11,0,26,10,9 XB-GENE-6251611,2,2,4,16,2,18 XB-GENE-6251613,593,279,462,808,410,249 @@ -4596,6 +4634,7 @@ XB-GENE-6252042,413,509,658,530,499,388 XB-GENE-6252055,693,579,756,836,771,458 XB-GENE-6252061,21,24,51,48,27,78 XB-GENE-6252065,27,18,27,31,29,18 +XB-GENE-6252072,0,0,0,35,7,38 XB-GENE-6252073,7527,8521,14838,10282,8969,8069 XB-GENE-6252075,15,21,21,24,22,16 XB-GENE-6252077,107,101,155,93,137,81 @@ -4621,6 +4660,7 @@ XB-GENE-6252130,34,34,61,26,15,30 XB-GENE-6252131,131,137,160,151,176,119 XB-GENE-6252134,49,48,66,58,48,45 XB-GENE-6252135,1,0,1,12,1,15 +XB-GENE-6252136,0,0,9,0,1,56 XB-GENE-6252137,1,2,30,2,3,37 XB-GENE-6252139,613,604,1046,664,671,494 XB-GENE-6252140,41,48,820,51,36,67 @@ -4708,6 +4748,7 @@ XB-GENE-6252357,47,57,76,47,69,46 XB-GENE-6252367,0,2,3,49,7,56 XB-GENE-6252370,796,798,1066,742,742,642 XB-GENE-6252384,28,41,137,32,31,114 +XB-GENE-6252388,0,0,0,35,7,35 XB-GENE-6252397,306,312,255,439,326,230 XB-GENE-6252399,17,19,34,21,21,19 XB-GENE-6252408,412,491,562,246,479,152 @@ -4855,6 +4896,8 @@ XB-GENE-6252843,148,173,286,242,204,198 XB-GENE-6252844,97,117,121,105,109,55 XB-GENE-6252851,495,426,534,494,530,323 XB-GENE-6252852,196,199,253,186,225,134 +XB-GENE-6252854,0,0,4,4,4,9 +XB-GENE-6252857,0,0,0,21,1,22 XB-GENE-6252871,292,298,218,292,347,97 XB-GENE-6252872,12,16,17,12,14,15 XB-GENE-6252875,6,2,11,6,10,4 @@ -5071,6 +5114,7 @@ XB-GENE-6253879,161,223,229,193,274,134 XB-GENE-6253882,118,80,126,93,81,89 XB-GENE-6253883,91,115,112,110,115,62 XB-GENE-6253884,434,496,591,552,555,349 +XB-GENE-6253886,0,0,0,2,1,20 XB-GENE-6253887,21,39,55,38,30,53 XB-GENE-6253888,588,793,936,685,769,588 XB-GENE-6253889,167,161,237,167,179,140 @@ -5199,6 +5243,7 @@ XB-GENE-6254092,24,34,35,26,36,22 XB-GENE-6254094,99,113,109,104,106,56 XB-GENE-6254095,7,6,15,10,10,10 XB-GENE-6254097,18,14,28,32,19,18 +XB-GENE-6254098,0,0,1,23,1,27 XB-GENE-6254103,39,49,82,41,52,50 XB-GENE-6254107,1152,1132,1118,1476,1239,902 XB-GENE-6254108,401,389,540,420,412,217 @@ -5240,6 +5285,7 @@ XB-GENE-6254210,7,13,8,9,15,7 XB-GENE-6254211,13,16,22,17,23,19 XB-GENE-6254212,459,439,511,583,532,253 XB-GENE-6254213,113,146,154,144,173,79 +XB-GENE-6254214,0,1,0,100,22,19 XB-GENE-6254216,735,572,867,815,663,538 XB-GENE-6254218,50,69,78,144,76,103 XB-GENE-6254219,486,604,548,642,683,431 @@ -5252,6 +5298,7 @@ XB-GENE-6254226,124,217,185,235,242,143 XB-GENE-6254227,4,1,8,1,8,3 XB-GENE-6254229,136,175,281,199,187,144 XB-GENE-6254232,65,69,107,67,70,51 +XB-GENE-6254236,0,8,4,4,8,0 XB-GENE-6254242,7,7,11,56,16,53 XB-GENE-6254244,713,815,1210,795,1051,708 XB-GENE-6254256,125,105,75,122,150,42 @@ -5281,6 +5328,7 @@ XB-GENE-6254299,25,24,33,29,23,14 XB-GENE-6254304,188,222,297,253,242,179 XB-GENE-6254305,88,90,117,98,106,55 XB-GENE-6254307,3,6,11,4,3,6 +XB-GENE-6254308,26,0,51,88,0,0 XB-GENE-6254312,41,40,64,41,56,44 XB-GENE-6254313,39,44,42,45,59,43 XB-GENE-6254317,53,51,44,63,78,42 @@ -5317,6 +5365,7 @@ XB-GENE-6254384,87,78,124,102,83,76 XB-GENE-6254385,11,9,21,15,10,26 XB-GENE-6254391,142,150,198,152,169,125 XB-GENE-6254392,8,6,11,12,9,4 +XB-GENE-6254394,0,0,0,73,6,63 XB-GENE-6254401,2,11,6,10,10,24 XB-GENE-6254406,385,393,540,358,391,250 XB-GENE-6254407,50,45,84,47,17,34 @@ -5353,6 +5402,7 @@ XB-GENE-6254464,155,199,450,216,217,352 XB-GENE-6254465,1056,1515,1927,1559,1789,1022 XB-GENE-6254466,81,72,110,90,72,101 XB-GENE-6254467,313,254,206,306,221,110 +XB-GENE-6254468,0,0,4,3,5,10 XB-GENE-6254472,152,175,271,178,222,159 XB-GENE-6254475,1023,873,1238,792,796,518 XB-GENE-6254478,968,1079,1666,1458,1388,1382 @@ -5487,6 +5537,7 @@ XB-GENE-6254870,154,210,257,217,195,171 XB-GENE-6254872,40,35,56,51,50,28 XB-GENE-6254873,21,22,26,22,21,23 XB-GENE-6254878,7,6,11,3,5,7 +XB-GENE-6254881,0,0,3,359,79,451 XB-GENE-6254884,171,166,205,150,194,121 XB-GENE-6254889,77,74,109,81,71,51 XB-GENE-6254892,56,67,85,75,73,63 @@ -5786,6 +5837,7 @@ XB-GENE-6255653,63,72,102,84,77,75 XB-GENE-6255657,33,52,62,48,60,40 XB-GENE-6255661,413,410,571,469,486,280 XB-GENE-6255663,129,118,280,109,109,108 +XB-GENE-6255665,0,42,71,0,42,85 XB-GENE-6255669,128,114,208,166,113,156 XB-GENE-6255670,2,9,1,3,6,10 XB-GENE-6255672,16,17,29,22,15,18 @@ -6156,6 +6208,7 @@ XB-GENE-6466458,306,214,405,386,235,272 XB-GENE-6466467,151,143,148,168,150,93 XB-GENE-6466521,2,17,18,26,20,38 XB-GENE-6466578,28,24,38,30,41,30 +XB-GENE-6466680,0,0,0,21,2,22 XB-GENE-6485591,3,1,1,23,13,37 XB-GENE-6485604,79,93,167,82,87,70 XB-GENE-6485637,135,111,246,221,142,208 @@ -6224,8 +6277,10 @@ XB-GENE-6487642,15,8,25,9,7,17 XB-GENE-6487743,1127,1140,1538,1449,1142,709 XB-GENE-6487851,189,235,291,249,186,120 XB-GENE-6487975,6,2,4,5,1,3 +XB-GENE-6488002,0,0,0,10,1,26 XB-GENE-6488146,6,23,8,16,24,0 XB-GENE-6488149,22,15,23,22,29,23 +XB-GENE-6488182,0,0,0,11,5,20 XB-GENE-6488221,540,669,1158,742,803,868 XB-GENE-6488249,114,101,165,106,119,92 XB-GENE-6488250,27,31,62,27,26,27 @@ -6279,6 +6334,7 @@ XB-GENE-6540652,6031,5494,6521,5853,6042,3093 XB-GENE-852658,447,452,680,528,473,378 XB-GENE-852734,21,37,37,28,40,29 XB-GENE-852749,28,26,26,38,36,20 +XB-GENE-852823,1,0,0,35,6,41 XB-GENE-852896,30,63,40,20,48,44 XB-GENE-852934,2,2,8,9,4,12 XB-GENE-853028,46,34,68,53,53,72 @@ -6315,6 +6371,7 @@ XB-GENE-864807,818,640,968,673,625,509 XB-GENE-864809,470,479,648,621,541,473 XB-GENE-864810,55,57,55,60,34,34 XB-GENE-864811,76,47,120,42,112,81 +XB-GENE-864813,0,0,1,77,19,59 XB-GENE-864814,11,24,36,37,15,22 XB-GENE-864816,60,85,115,85,52,63 XB-GENE-864819,378,297,388,393,263,272 @@ -6338,6 +6395,7 @@ XB-GENE-864869,582,648,773,626,753,508 XB-GENE-864871,483,498,587,587,586,368 XB-GENE-864873,15,14,17,24,13,12 XB-GENE-864883,6,19,16,12,8,14 +XB-GENE-864885,0,0,0,14,5,14 XB-GENE-864886,9,8,9,6,8,8 XB-GENE-864891,16,67,9,30,38,42 XB-GENE-864893,35,35,83,49,57,73 @@ -6360,6 +6418,7 @@ XB-GENE-864943,45,59,44,59,54,30 XB-GENE-864944,78,46,69,120,53,56 XB-GENE-864945,53,41,41,49,41,35 XB-GENE-864949,4,8,11,11,11,17 +XB-GENE-864950,3,0,12,0,2,5 XB-GENE-864955,14,14,18,16,19,14 XB-GENE-864959,4,7,62,11,16,28 XB-GENE-864966,16,35,27,45,11,26 @@ -6377,6 +6436,7 @@ XB-GENE-864994,125,154,227,142,191,137 XB-GENE-864997,34,32,51,34,38,29 XB-GENE-865001,3,15,26,15,23,16 XB-GENE-865002,19,3,24,14,9,18 +XB-GENE-865003,0,0,0,68,49,43 XB-GENE-865004,1,0,2,10,2,23 XB-GENE-865007,2,1,19,3,0,2 XB-GENE-865009,209,190,322,216,226,202 @@ -6417,6 +6477,7 @@ XB-GENE-865079,18,32,55,39,23,42 XB-GENE-865080,31,24,45,41,35,29 XB-GENE-865084,226,258,3444,728,251,1604 XB-GENE-865094,3,5,9,7,4,4 +XB-GENE-865098,0,1,0,48,4,62 XB-GENE-865100,360,390,674,422,400,357 XB-GENE-865101,234,333,371,354,350,312 XB-GENE-865103,24,15,35,17,34,22 @@ -6428,6 +6489,7 @@ XB-GENE-865114,170,183,241,173,154,220 XB-GENE-865118,89,92,143,91,120,24 XB-GENE-865119,60,80,112,73,78,65 XB-GENE-865121,388,446,632,497,486,362 +XB-GENE-865122,0,1,0,40,12,44 XB-GENE-865123,59,64,87,101,84,59 XB-GENE-865124,22,22,43,28,22,28 XB-GENE-865126,115,131,151,83,185,49 @@ -6453,6 +6515,7 @@ XB-GENE-865161,17,26,36,20,21,31 XB-GENE-865168,133,137,257,148,148,164 XB-GENE-865171,33,51,87,127,64,109 XB-GENE-865172,86,59,156,89,71,59 +XB-GENE-865180,0,0,0,19,5,32 XB-GENE-865183,31,30,45,34,34,27 XB-GENE-865192,74,82,113,98,94,88 XB-GENE-865193,2,6,9,2,9,4 @@ -6496,6 +6559,7 @@ XB-GENE-865270,279,304,499,389,303,289 XB-GENE-865273,590,517,687,586,550,385 XB-GENE-865275,27,43,41,46,41,37 XB-GENE-865279,734,775,926,867,791,471 +XB-GENE-865280,0,0,1,10,6,47 XB-GENE-865283,259,314,646,500,377,596 XB-GENE-865284,287,261,338,294,310,183 XB-GENE-865285,4345,4093,5497,4585,3945,2711 @@ -6508,6 +6572,7 @@ XB-GENE-865299,2,12,4,7,2,3 XB-GENE-865300,58,75,82,91,71,63 XB-GENE-865304,470,563,496,575,676,436 XB-GENE-865306,13,17,97,12,14,20 +XB-GENE-865309,0,0,0,56,9,66 XB-GENE-865310,10,9,12,10,15,8 XB-GENE-865311,36,36,29,44,36,16 XB-GENE-865312,159,112,139,173,125,121 @@ -6536,6 +6601,8 @@ XB-GENE-865366,45,57,88,65,57,63 XB-GENE-865367,326,273,454,573,280,303 XB-GENE-865369,66,80,140,84,70,82 XB-GENE-865370,133,97,224,161,172,156 +XB-GENE-865372,0,0,3,24,14,24 +XB-GENE-865376,0,0,0,39,3,32 XB-GENE-865378,18,30,75,41,51,62 XB-GENE-865379,4,2,20,5,4,5 XB-GENE-865383,1,0,10,31,7,33 @@ -6556,6 +6623,7 @@ XB-GENE-865418,57,36,69,48,49,45 XB-GENE-865423,22,22,17,22,20,11 XB-GENE-865425,331,410,419,389,393,256 XB-GENE-865427,5,7,13,11,7,12 +XB-GENE-865431,0,1,0,55,22,50 XB-GENE-865434,119,226,157,315,351,180 XB-GENE-865435,198,237,154,210,281,112 XB-GENE-865436,288,232,288,283,245,150 @@ -6570,6 +6638,7 @@ XB-GENE-865454,26,31,63,36,40,51 XB-GENE-865455,8,11,18,17,9,11 XB-GENE-865457,88,72,124,100,108,73 XB-GENE-865461,102,142,161,142,151,98 +XB-GENE-865462,13,0,0,21,0,18 XB-GENE-865463,188,213,284,217,191,142 XB-GENE-865464,8,13,13,6,9,3 XB-GENE-865468,4,9,0,4,5,1 @@ -6612,6 +6681,7 @@ XB-GENE-865541,10,0,11,15,7,11 XB-GENE-865543,106,106,84,164,103,49 XB-GENE-865546,258,265,231,296,391,164 XB-GENE-865553,4,2,4,8,8,2 +XB-GENE-865554,0,0,0,43,8,35 XB-GENE-865555,189,229,244,295,247,119 XB-GENE-865560,2450,2497,2652,3160,2790,1802 XB-GENE-865562,342,290,168,220,287,118 @@ -6637,6 +6707,7 @@ XB-GENE-865602,43,54,86,51,77,66 XB-GENE-865608,87,138,136,135,136,56 XB-GENE-865610,71,109,130,98,95,87 XB-GENE-865613,691,679,661,749,697,421 +XB-GENE-865614,0,0,0,28,4,70 XB-GENE-865617,4,7,17,15,10,17 XB-GENE-865618,103,88,112,126,87,70 XB-GENE-865622,70,70,113,75,90,98 @@ -6815,6 +6886,7 @@ XB-GENE-866002,39,36,60,46,33,36 XB-GENE-866005,330,383,562,450,424,369 XB-GENE-866007,65,73,107,77,94,75 XB-GENE-866008,425,554,533,391,462,363 +XB-GENE-866009,1,0,7,0,0,20 XB-GENE-866011,78807,80257,117945,73766,76585,61531 XB-GENE-866013,238,496,388,409,486,303 XB-GENE-866017,104,128,176,131,164,147 @@ -6910,6 +6982,7 @@ XB-GENE-866199,48,49,44,44,58,37 XB-GENE-866203,17,31,24,75,73,47 XB-GENE-866205,205,186,288,244,211,173 XB-GENE-866208,658,609,525,711,680,290 +XB-GENE-866210,3,0,1,4,0,29 XB-GENE-866212,296,281,314,322,342,182 XB-GENE-866214,454,514,702,614,603,485 XB-GENE-866217,117,158,278,163,159,172 @@ -7055,6 +7128,7 @@ XB-GENE-866565,263,187,280,251,242,127 XB-GENE-866566,49,38,94,56,53,57 XB-GENE-866569,748,752,889,767,694,448 XB-GENE-866571,254,282,270,286,296,185 +XB-GENE-866575,0,0,3,13,0,21 XB-GENE-866576,39,38,56,46,58,41 XB-GENE-866577,2,3,11,4,5,13 XB-GENE-866578,9,10,21,10,11,10 @@ -7063,6 +7137,7 @@ XB-GENE-866582,24,24,26,19,14,13 XB-GENE-866587,35,40,75,37,45,34 XB-GENE-866594,73,64,94,97,67,55 XB-GENE-866596,52,54,78,57,52,36 +XB-GENE-866599,0,0,0,14,9,9 XB-GENE-866600,336,404,634,508,467,435 XB-GENE-866603,182,173,227,177,191,118 XB-GENE-866605,79,63,108,102,79,65 @@ -7109,6 +7184,7 @@ XB-GENE-876432,21,25,23,16,19,13 XB-GENE-876461,121,155,248,144,181,134 XB-GENE-876487,3482,2707,3291,3889,3070,2438 XB-GENE-876504,15,11,22,23,12,26 +XB-GENE-876576,0,0,7,1,4,36 XB-GENE-876616,4,10,8,6,16,5 XB-GENE-876631,105,157,151,255,213,153 XB-GENE-876665,5,2,5,3,5,4 @@ -7150,6 +7226,7 @@ XB-GENE-919989,14,19,25,21,14,21 XB-GENE-920005,990,1034,1304,1181,1076,714 XB-GENE-920037,177,183,191,223,228,138 XB-GENE-920053,767,1049,1265,1225,1095,896 +XB-GENE-920126,0,0,0,11,4,15 XB-GENE-920197,165,190,243,189,191,132 XB-GENE-920224,75,177,193,176,155,176 XB-GENE-920250,9,14,11,17,17,13 @@ -7175,6 +7252,7 @@ XB-GENE-920761,12,10,16,18,14,6 XB-GENE-920773,15,13,25,36,24,47 XB-GENE-920796,1916,1927,2339,2347,1500,986 XB-GENE-920812,62,49,103,63,64,64 +XB-GENE-920837,0,0,1,10,4,23 XB-GENE-920851,165,208,312,212,212,179 XB-GENE-920863,36,45,102,59,57,84 XB-GENE-920952,325,310,204,387,375,98 @@ -7182,6 +7260,7 @@ XB-GENE-921352,64,85,136,119,94,93 XB-GENE-921398,8,9,18,7,12,8 XB-GENE-921424,94,120,178,120,133,132 XB-GENE-921439,264,239,352,287,268,232 +XB-GENE-921463,0,0,9,2,0,12 XB-GENE-921475,1511,930,2633,1368,917,1374 XB-GENE-921543,44,71,92,71,62,76 XB-GENE-921605,8,8,15,11,8,9 @@ -7577,6 +7656,7 @@ XB-GENE-946821,35,32,26,42,33,15 XB-GENE-946866,308,330,463,303,367,213 XB-GENE-946923,848,953,1087,1090,1020,764 XB-GENE-946933,92,236,218,241,203,162 +XB-GENE-946946,0,0,1,6,3,12 XB-GENE-946957,20,7,34,18,17,21 XB-GENE-946968,52,75,130,87,93,79 XB-GENE-946990,201,204,273,253,269,189 @@ -7906,6 +7986,7 @@ XB-GENE-953759,131,127,255,155,133,105 XB-GENE-953778,40,57,62,56,43,49 XB-GENE-953788,198,196,327,265,241,154 XB-GENE-953814,45,51,75,49,47,63 +XB-GENE-953838,4,0,17,0,0,6 XB-GENE-953851,69,48,54,75,41,36 XB-GENE-953859,38,35,59,43,42,29 XB-GENE-953870,77,80,108,73,92,49 @@ -7926,6 +8007,7 @@ XB-GENE-954242,40,61,56,57,55,37 XB-GENE-954255,43,72,176,53,90,100 XB-GENE-954266,199,165,217,192,193,122 XB-GENE-954290,197,230,283,199,272,191 +XB-GENE-954301,1,0,21,0,0,15 XB-GENE-954315,27,18,21,21,25,12 XB-GENE-954324,207,233,198,208,291,120 XB-GENE-954333,77,80,131,111,103,113 @@ -8111,6 +8193,7 @@ XB-GENE-958354,105,122,170,168,130,91 XB-GENE-958367,562,790,937,784,791,619 XB-GENE-958379,265,353,537,320,417,331 XB-GENE-958409,21,21,32,27,26,18 +XB-GENE-958420,0,1,2,25,0,12 XB-GENE-958433,10,7,13,5,5,2 XB-GENE-958447,185,189,396,228,213,260 XB-GENE-958472,8,14,16,19,11,15 @@ -8504,6 +8587,7 @@ XB-GENE-966454,1096,1024,1188,1237,1166,870 XB-GENE-966475,150,151,194,153,156,103 XB-GENE-966491,140,165,216,174,172,124 XB-GENE-966533,99,98,148,114,102,133 +XB-GENE-966542,1,0,1,0,0,43 XB-GENE-966569,346,359,559,497,327,334 XB-GENE-966589,191,210,209,180,195,129 XB-GENE-966600,234,340,408,385,433,456 @@ -8704,6 +8788,7 @@ XB-GENE-971067,54,56,73,56,58,39 XB-GENE-971077,300,310,561,455,403,351 XB-GENE-971102,133,164,174,131,159,99 XB-GENE-971113,41,63,110,81,90,75 +XB-GENE-971141,0,0,0,15,1,17 XB-GENE-971154,682,833,994,1034,999,792 XB-GENE-971204,423,428,462,505,477,269 XB-GENE-971217,212,204,326,236,228,179 @@ -8742,6 +8827,7 @@ XB-GENE-971963,14,19,51,20,23,26 XB-GENE-972017,23,32,45,32,35,31 XB-GENE-972027,71,63,76,59,57,38 XB-GENE-972047,49,43,59,58,49,50 +XB-GENE-972091,0,0,0,5,5,29 XB-GENE-972107,27,21,41,44,20,23 XB-GENE-972147,128,137,200,170,121,121 XB-GENE-972163,720,736,962,979,829,586 @@ -8798,6 +8884,7 @@ XB-GENE-973123,110,93,184,108,86,98 XB-GENE-973167,64,67,107,91,83,61 XB-GENE-973199,22,26,52,21,22,39 XB-GENE-973235,370,562,624,688,584,552 +XB-GENE-973248,0,0,1,4,9,7 XB-GENE-973276,106,143,147,159,209,108 XB-GENE-973285,34,42,41,39,56,29 XB-GENE-973299,70,115,151,117,139,159 @@ -8818,6 +8905,7 @@ XB-GENE-973595,176,169,206,184,192,147 XB-GENE-973623,732,684,1089,1000,888,744 XB-GENE-973633,118,134,157,154,128,77 XB-GENE-973644,1079,1082,1467,1289,1204,775 +XB-GENE-973679,0,1,18,0,1,27 XB-GENE-973722,33,36,34,36,35,23 XB-GENE-973755,47,11,25,59,25,40 XB-GENE-973767,129,204,243,208,206,147 @@ -8913,6 +9001,7 @@ XB-GENE-976017,88,96,88,129,82,55 XB-GENE-976029,254,303,361,315,323,223 XB-GENE-976038,114,155,219,175,141,168 XB-GENE-976062,28,37,72,60,32,38 +XB-GENE-976075,0,23,16,2,0,52 XB-GENE-976090,88,91,124,114,111,86 XB-GENE-976119,178,214,282,231,199,181 XB-GENE-976131,10,16,21,11,17,13 @@ -9079,6 +9168,7 @@ XB-GENE-979454,7,8,14,12,5,9 XB-GENE-979461,31,32,43,25,58,27 XB-GENE-979490,137,121,219,167,148,125 XB-GENE-979502,127,159,237,141,176,145 +XB-GENE-979514,0,0,2,3,7,17 XB-GENE-979529,23,20,24,24,21,10 XB-GENE-979568,167,137,277,204,184,205 XB-GENE-979588,27,18,63,33,44,33 @@ -9317,6 +9407,7 @@ XB-GENE-984831,88,81,97,89,95,49 XB-GENE-984880,66,68,107,88,82,62 XB-GENE-984894,5,6,10,6,4,4 XB-GENE-984903,528,527,681,579,533,366 +XB-GENE-984929,23,44,0,6,19,0 XB-GENE-984941,148,136,257,171,152,170 XB-GENE-984948,132,150,152,148,139,80 XB-GENE-984964,175,170,257,191,164,172 @@ -9373,6 +9464,7 @@ XB-GENE-985937,33,36,45,46,59,38 XB-GENE-985949,125,112,129,134,117,73 XB-GENE-985968,25,37,25,40,35,19 XB-GENE-986009,47,58,80,66,67,59 +XB-GENE-986018,0,11,12,6,9,0 XB-GENE-986031,206,176,302,260,217,169 XB-GENE-986041,12,16,15,20,15,10 XB-GENE-986099,224,248,328,365,293,278 @@ -9672,6 +9764,7 @@ XB-GENE-992253,38,46,34,55,44,24 XB-GENE-992262,55,80,214,76,74,118 XB-GENE-992269,5,2,13,4,7,4 XB-GENE-992279,45,57,58,61,82,54 +XB-GENE-992308,1,0,21,0,2,2 XB-GENE-992340,160,201,221,237,218,169 XB-GENE-992355,77,38,194,78,29,86 XB-GENE-992367,69,75,73,75,65,47 @@ -9851,6 +9944,7 @@ XB-GENE-996047,54,41,79,89,39,84 XB-GENE-996065,90,98,253,80,165,139 XB-GENE-996110,2361,2223,3090,2762,2540,1853 XB-GENE-996125,2018,2309,1783,2076,2342,998 +XB-GENE-996134,0,0,14,0,1,15 XB-GENE-996149,22,14,43,25,26,18 XB-GENE-996159,29,39,57,46,47,42 XB-GENE-996170,33,44,55,36,49,33 @@ -9960,6 +10054,7 @@ XB-GENE-998249,188,275,193,221,276,164 XB-GENE-998265,72,82,131,108,93,106 XB-GENE-998277,194,125,315,211,212,179 XB-GENE-998293,107,123,133,122,110,108 +XB-GENE-998305,0,0,14,0,13,6 XB-GENE-998330,174,185,289,240,204,222 XB-GENE-998343,1104,1069,1137,1253,1131,714 XB-GENE-998363,20,24,26,24,26,14 diff --git a/omics/week-3/data-processed/s30_summary_gene_filtered.csv b/omics/week-3/data-processed/s30_summary_gene_filtered.csv index b73cacd..62bb0b6 100644 --- a/omics/week-3/data-processed/s30_summary_gene_filtered.csv +++ b/omics/week-3/data-processed/s30_summary_gene_filtered.csv @@ -44,6 +44,7 @@ XB-GENE-1001088,253,262.5,85.43242943987956,312.5,267.5,335.5,468,1875,0 XB-GENE-1001113,139,149.5,32.335738742141025,168,152.5,183.25,222,1008,0 XB-GENE-1001131,29,32.25,14.932068398807537,45.166666666666664,45.5,55.75,64,271,0 XB-GENE-1001158,155,215,48.63914747059889,231.83333333333334,228.5,263.75,293,1391,0 +XB-GENE-1001182,0,0.5,4.4907311951024935,3.8333333333333335,2,7.25,10,23,2 XB-GENE-1001202,113,126.25,54.4046566634389,172.33333333333334,171.5,204.75,251,1034,0 XB-GENE-1001213,106,113,33.102366481366055,137.16666666666666,133.5,144.25,196,823,0 XB-GENE-1001247,30,46.75,14.972196454317137,53.833333333333336,56,63,72,323,0 @@ -298,6 +299,7 @@ XB-GENE-1007210,81,93,21.848722311994965,110.16666666666667,116,126.25,133,661,0 XB-GENE-1007229,97,144.25,44.36965930302674,166.33333333333334,174.5,189.75,223,998,0 XB-GENE-1007241,184,200.75,43.88811532370315,234.16666666666666,231.5,260.75,297,1405,0 XB-GENE-1007252,164,244.25,47.64206824505698,247.83333333333334,245.5,279,298,1487,0 +XB-GENE-1007263,0,0.25,8.280499179799891,4.166666666666667,1,1.75,21,25,2 XB-GENE-1007284,71,85.25,12.361229712289955,90,89,99.5,104,540,0 XB-GENE-1007301,96,232.25,75.82523766310705,240.66666666666666,269,287,297,1444,0 XB-GENE-1007318,294,369,62.83205126897153,389.6666666666667,382,423.5,478,2338,0 @@ -435,6 +437,7 @@ XB-GENE-1010862,129,224,64.09680179228913,237,247.5,253.75,326,1422,0 XB-GENE-1010880,47,62.5,13.9522996909709,68.66666666666667,68.5,79.75,84,412,0 XB-GENE-1010935,49,50.25,17.204650534085253,58,51.5,52.75,93,348,0 XB-GENE-1010966,27,29.25,7.201851613763412,33.666666666666664,32,34.75,47,202,0 +XB-GENE-1010995,0,6,20.68574388316746,24.5,28,41.75,46,147,2 XB-GENE-1011022,23,28,6.306081720582652,31.166666666666668,30,34.25,41,187,0 XB-GENE-1011062,377,463.75,92.6270298922872,501.1666666666667,494.5,520.75,658,3007,0 XB-GENE-1011071,30,36.25,11.303391821336932,41.833333333333336,38,45,62,251,0 @@ -722,6 +725,7 @@ XB-GENE-1018177,22,24,7.57407860182786,28.833333333333332,27.5,29.5,43,173,0 XB-GENE-1018199,204,231.25,30.07158126869952,248.5,252.5,266.25,287,1491,0 XB-GENE-1018219,4662,9163.75,2630.619065289892,9401.333333333334,9512.5,11007.25,12168,56408,0 XB-GENE-1018237,377,739.75,187.53630759580042,736.3333333333334,771.5,838.5,908,4418,0 +XB-GENE-1018260,0,0,6.772493386240157,4.666666666666667,1,8,16,28,3 XB-GENE-1018301,359,373,128.1244186978683,455.6666666666667,423.5,458.25,702,2734,0 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XB-GENE-966569,327,337,98.88511852987115,403.6666666666667,352.5,462.5,559,2422,0 XB-GENE-966589,129,182.75,29.984440409430135,185.66666666666666,193,205.5,210,1114,0 XB-GENE-966600,234,351.25,80.26705426263007,376,396.5,426.75,456,2256,0 @@ -8704,6 +8788,7 @@ XB-GENE-971067,39,54.5,10.825894882179487,56,56,57.5,73,336,0 XB-GENE-971077,300,320.25,99.3874572904784,396.6666666666667,377,442,561,2380,0 XB-GENE-971102,99,131.5,27.703188745461535,143.33333333333334,146,162.75,174,860,0 XB-GENE-971113,41,66,23.53437202618049,76.66666666666667,78,87.75,110,460,0 +XB-GENE-971141,0,0,8.167006795638168,5.5,0.5,11.5,17,33,3 XB-GENE-971154,682,802.25,141.09854712221525,889,913.5,997.75,1034,5334,0 XB-GENE-971204,269,424.25,83.41382779052084,427.3333333333333,445,473.25,505,2564,0 XB-GENE-971217,179,206,50.70075607588773,230.83333333333334,220,234,326,1385,0 @@ -8742,6 +8827,7 @@ XB-GENE-971963,14,19.25,13.126309458488324,25.5,21.5,25.25,51,153,0 XB-GENE-972017,23,31.25,7.127411872482185,33,32,34.25,45,198,0 XB-GENE-972027,38,57.5,13.246383154154445,60.666666666666664,61,69,76,364,0 XB-GENE-972047,43,49,6.0882400303098,51.333333333333336,49.5,56,59,308,0 +XB-GENE-972091,0,0,11.291589790636214,6.5,2.5,5,29,39,3 XB-GENE-972107,20,21.5,10.519822558706334,29.333333333333332,25,37.5,44,176,0 XB-GENE-972147,121,122.75,32.083744586108814,146.16666666666666,132.5,161.75,200,877,0 XB-GENE-972163,586,724,151.91708264708086,802,782.5,928.75,979,4812,0 @@ -8798,6 +8884,7 @@ XB-GENE-973123,86,94.25,35.85758869007601,113.16666666666667,103,109.5,184,679,0 XB-GENE-973167,61,64.75,18.093276836069986,78.83333333333333,75,89,107,473,0 XB-GENE-973199,21,22,12.564500255349063,30.333333333333332,24,35.75,52,182,0 XB-GENE-973235,370,554.5,106.91803714372364,563.3333333333334,573,614,688,3380,0 +XB-GENE-973248,0,0.25,3.8340579025361627,3.5,2.5,6.25,9,21,2 XB-GENE-973276,106,116.75,37.919212368754,145.33333333333334,145,156,209,872,0 XB-GENE-973285,29,35.25,9.152413160837238,40.166666666666664,40,41.75,56,241,0 XB-GENE-973299,70,115.5,32.30118676870351,125.16666666666667,128,148,159,751,0 @@ -8818,6 +8905,7 @@ XB-GENE-973595,147,170.75,20.27806696901852,179,180,190,206,1074,0 XB-GENE-973623,684,735,163.43367666018733,856.1666666666666,816,972,1089,5137,0 XB-GENE-973633,77,120.5,29.168476134347504,128,131,149,157,768,0 XB-GENE-973644,775,1079.75,233.67213498118826,1149.3333333333333,1143,1267.75,1467,6896,0 +XB-GENE-973679,0,0.25,11.72035266818651,7.833333333333333,1,13.75,27,47,2 XB-GENE-973722,23,33.25,4.9564772436345015,32.833333333333336,34.5,35.75,36,197,0 XB-GENE-973755,11,25,17.432727841620196,34.5,32.5,45.25,59,207,0 XB-GENE-973767,129,161.25,42.786680170352085,189.5,205,207.5,243,1137,0 @@ -8913,6 +9001,7 @@ XB-GENE-976017,55,83.5,23.888630489558555,89.66666666666667,88,94,129,538,0 XB-GENE-976029,223,266.25,49.91092064869171,296.5,309,321,361,1779,0 XB-GENE-976038,114,144.5,35.34968175245712,162,161.5,173.25,219,972,0 XB-GENE-976062,28,33.25,17.455658108475888,44.5,37.5,54.5,72,267,0 +XB-GENE-976075,0,0.5,20.255863348670182,15.5,9,21.25,52,93,2 XB-GENE-976090,86,88.75,16.00833116432399,102.33333333333333,101,113.25,124,614,0 XB-GENE-976119,178,185.5,38.788744071787974,214.16666666666666,206.5,226.75,282,1285,0 XB-GENE-976131,10,11.5,4.131182235954578,14.666666666666666,14.5,16.75,21,88,0 @@ -9079,6 +9168,7 @@ XB-GENE-979454,5,7.25,3.3115957885386114,9.166666666666666,8.5,11.25,14,55,0 XB-GENE-979461,25,28,12.457929201917949,36,31.5,40.25,58,216,0 XB-GENE-979490,121,128,36.44402100025005,152.83333333333334,142.5,162.25,219,917,0 XB-GENE-979502,127,142,39.387392229832464,164.16666666666666,152,171.75,237,985,0 +XB-GENE-979514,0,0.5,6.493586579592718,4.833333333333333,2.5,6,17,29,2 XB-GENE-979529,10,20.25,5.316640543300503,20.333333333333332,22,23.75,24,122,0 XB-GENE-979568,137,171.25,47.26803006966407,195.66666666666666,194,204.75,277,1174,0 XB-GENE-979588,18,28.5,15.59059545580818,36.333333333333336,33,41.25,63,218,0 @@ -9317,6 +9407,7 @@ XB-GENE-984831,49,82.75,17.668238923748646,83.16666666666667,88.5,93.5,97,499,0 XB-GENE-984880,62,66.5,17.04601615236436,78.83333333333333,75,86.5,107,473,0 XB-GENE-984894,4,4.25,2.228601953392904,5.833333333333333,5.5,6,10,35,0 XB-GENE-984903,366,527.25,101.90910983158801,535.6666666666666,530.5,567.5,681,3214,0 +XB-GENE-984929,0,1.5,17.037214169771612,15.333333333333334,12.5,22,44,92,2 XB-GENE-984941,136,149,43.59204820453687,172.33333333333334,161,170.75,257,1034,0 XB-GENE-984948,80,133.75,27.274530243434075,133.5,143.5,149.5,152,801,0 XB-GENE-984964,164,170.5,34.913703135970366,188.16666666666666,173.5,187,257,1129,0 @@ -9373,6 +9464,7 @@ XB-GENE-985937,33,36.5,9.410986487434071,42.833333333333336,41.5,45.75,59,257,0 XB-GENE-985949,73,113.25,22.063544592834578,115,121,128,134,690,0 XB-GENE-985968,19,25,8.304617189652191,30.166666666666668,30,36.5,40,181,0 XB-GENE-986009,47,58.25,11.052903087726168,62.833333333333336,62.5,66.75,80,377,0 +XB-GENE-986018,0,1.5,5.316640543300503,6.333333333333333,7.5,10.5,12,38,2 XB-GENE-986031,169,183.5,51.08685414729182,221.66666666666666,211.5,249.25,302,1330,0 XB-GENE-986041,10,12.75,3.444802848737017,14.666666666666666,15,15.75,20,88,0 XB-GENE-986099,224,255.5,51.651395592632994,289.3333333333333,285.5,319.25,365,1736,0 @@ -9672,6 +9764,7 @@ XB-GENE-992253,24,35,10.703581954965667,40.166666666666664,41,45.5,55,241,0 XB-GENE-992262,55,74.5,58.22170271184678,102.83333333333333,78,108.5,214,617,0 XB-GENE-992269,2,4,3.8686776379877745,5.833333333333333,4.5,6.5,13,35,0 XB-GENE-992279,45,54.75,12.30853362509117,59.5,57.5,60.25,82,357,0 +XB-GENE-992308,0,0.25,8.2138095100061,4.333333333333333,1.5,2,21,26,2 XB-GENE-992340,160,177,30.62678566222711,201,209.5,220.25,237,1206,0 XB-GENE-992355,29,47.75,58.87161172132683,83.66666666666667,77.5,84,194,502,0 XB-GENE-992367,47,66,10.68955876856789,67.33333333333333,71,74.5,75,404,0 @@ -9851,6 +9944,7 @@ XB-GENE-996047,39,44.25,22.37558192911788,64.33333333333333,66.5,82.75,89,386,0 XB-GENE-996065,80,92,65.14829237977001,137.5,118.5,158.5,253,825,0 XB-GENE-996110,1853,2257.5,430.8432429550219,2471.5,2450.5,2706.5,3090,14829,0 XB-GENE-996125,998,1841.75,496.4256238350313,1921,2047,2250.75,2342,11526,0 +XB-GENE-996134,0,0,7.37563556583431,5,0.5,10.75,15,30,3 XB-GENE-996149,14,19,10.03327796219494,24.666666666666668,23.5,25.75,43,148,0 XB-GENE-996159,29,39.75,9.309493362512628,43.333333333333336,44,46.75,57,260,0 XB-GENE-996170,33,33.75,9.157874571463985,41.666666666666664,40,47.75,55,250,0 @@ -9960,6 +10054,7 @@ XB-GENE-998249,164,189.25,47.009573493066284,219.5,207,261.5,276,1317,0 XB-GENE-998265,72,84.75,21.011108173217963,98.66666666666667,99.5,107.5,131,592,0 XB-GENE-998277,125,182.75,62.25110440787376,206,202.5,211.75,315,1236,0 XB-GENE-998293,107,108.5,10.457851914550456,117.16666666666667,116,122.75,133,703,0 +XB-GENE-998305,0,0,6.6257075093909785,5.5,3,11.25,14,33,3 XB-GENE-998330,174,189.75,41.84734161210243,219,213,235.5,289,1314,0 XB-GENE-998343,714,1077.75,184.1564552221833,1068,1117.5,1135.5,1253,6408,0 XB-GENE-998363,14,21,4.633213427705081,22.333333333333332,24,25.5,26,134,0 diff --git a/omics/week-3/data-processed/s30_summary_samp.csv b/omics/week-3/data-processed/s30_summary_samp.csv new file mode 100644 index 0000000..8042175 --- /dev/null +++ b/omics/week-3/data-processed/s30_summary_samp.csv @@ -0,0 +1,7 @@ +sample,min,lowerq,mean,median,upperq,max,n_zero +S30_C_5,0,14,317.13957790296814,70,205,101746,1340 +S30_C_6,0,14,335.8430169006979,75,220,118708,1361 +S30_C_A,0,23,426.2883208610107,107,301,117945,998 +S30_F_5,0,19,376.2443454132683,88,251,117573,1210 +S30_F_6,0,17,376.49852854620366,84,246,130672,1199 +S30_F_A,0,16,260.43143025309007,69,187,61531,963 diff --git a/omics/week-3/overview.qmd b/omics/week-3/overview.qmd index 24cd8b6..b9325a2 100644 --- a/omics/week-3/overview.qmd +++ b/omics/week-3/overview.qmd @@ -1,22 +1,29 @@ --- title: "Overview" subtitle: "Omics 1: Hello data!" +toc: true +toc-location: right --- -xxxxx +This week you will meet your data. The independent study will concisely cover how these data were generated and how they have been processed before being given to you. There will also be an overview of the analysis we will carry out over three workshops. +In the workshop, you will learn what steps to take to get a good understanding of ’omics data before you consider any statistical analysis. This is an often overlooked, but very valuable and informative, part of any data pipeline. It gives you the deep understanding of the data structures and values that you will need to code and trouble-shoot code, allows you to spot failed or problematic samples and informs your decisions on quality control. + ### Learning objectives -- dd -- dd. -- dd -- d +The successful student will be able to: + +- explore 'omics data to find the number of rows and columns and know how these correspond to samples and variables +- explore the distribution of expression measures across whole data sets, across variables and across samples by summarising and plotting +- explain what distributions are expected and interpret the distributions they have +- explain on what basis we might filter out variables or samples +- import, explore and filter 'omics data reproducibly so they can understand and reuse their code in the future ### Instructions 1. [Prepare](study_before_workshop.qmd) - i. πŸ“– Read how the data were generated and how they have been processed so far. + i. πŸ“– Read how the data were generated and how they have been processed so far, insstall 2. [Workshop](workshop.qmd) diff --git a/omics/week-3/study_after_workshop.qmd b/omics/week-3/study_after_workshop.qmd index 5722ccd..d88995e 100644 --- a/omics/week-3/study_after_workshop.qmd +++ b/omics/week-3/study_after_workshop.qmd @@ -1,6 +1,8 @@ --- title: "Independent Study to consolidate this week" subtitle: "Core 1" +toc: true +toc-location: right format: html: code-fold: true diff --git a/omics/week-3/study_before_workshop.qmd b/omics/week-3/study_before_workshop.qmd index 14a635a..f63d162 100644 --- a/omics/week-3/study_before_workshop.qmd +++ b/omics/week-3/study_before_workshop.qmd @@ -19,37 +19,43 @@ editor: ## Omics workshops +What the data are and something about what has been done to the raw data to get get. + + - 🐸 the difference between the control and the FGF treated sibling at S30 - 🐭 the difference between HSPC and Prog cells - πŸ‚ ??????? -See later workshops. +## Aims + +- find important genes +- what is 'important' + - expressed + - differentially expressed i.e., which genes are significantly higher in one group vs another + ## Sequence Data +- The raw data are "reads" from a sequencing machine. Reads are short sequences of DNA or RNA. + + +- The reads are aligned to a reference genome or transcriptome. The reads are then counted to quantify the expression of each gene. The counts are normalised to allow comparison between samples. - reads - quality control - align/pseudoalign - quantify - normalise -## Aims - -- find important genes -- what is 'important' - - expressed - - differentially expressed i.e., which genes are significantly higher in one group vs another ## What is a read - FASTQ format files - sequences and information about each sequence's read accuracy -![](images/fastaq_file_format.png) ## Differential expression @@ -62,11 +68,11 @@ See later workshops. Cells were sorted using flow cytometry on the basis of cell surface markers. There are three cell types: -- long-term haematopoetic stem cells (LT-HSCs) defined as : Lineage^-^ ckit^+^ Sca1^+^ CD34^-^ Flk2^-^ +- long-term haematopoetic stem cells (LT-HSCs) -- haematopoetic stem and progenitor cells (HSPCs) defined as : Lineage^-^ Sca1^+^ ckit^+^ +- haematopoetic stem and progenitor cells (HSPCs) -- progenitor cells (Progs) defined as : Lineage^-^ Sca1^-^ ckit^+^ +- progenitor cells (Progs) Each cell is then sequenced to quantify all the transcripts in each cell. different transcripts (genes) were identified. @@ -156,3 +162,7 @@ Each cell is then sequenced to quantify all the transcripts in each cell. differ 4. Interpret the biology by reporting on a few group of genes and the processes in which they are involved. 5. Report on your chosen genes and explain why you think they are good candidates for follow up work + + +## revise pivot longer +## revise pivot longer \ No newline at end of file diff --git a/omics/week-3/workshop.qmd b/omics/week-3/workshop.qmd index 706b515..b4c51a2 100644 --- a/omics/week-3/workshop.qmd +++ b/omics/week-3/workshop.qmd @@ -168,8 +168,8 @@ s30 |> ``` This data is very skewed - there are so many low values that we can't -see the tiny bars for the higher values. Logging the counts is a way -to make the distribution more visible. +see the tiny bars for the higher values. Logging the counts is a way to +make the distribution more visible. 🎬 Repeat the plot on log of the counts. @@ -190,6 +190,12 @@ would expect the distribution of counts to be roughly log normal because this is expression of *all* the genes in the genome[^1]. That small peak near the low end suggests that these lower counts might be anomalies. +[^1]: This a result of the [Central limit + theorem](https://en.wikipedia.org/wiki/Central_limit_theorem),one + consequence of which is that adding together lots of distributions - + whatever distributions they are - will tend to a normal + distribution. + The excess number of low counts indicates we might want to create a cut off for quality control. The removal of low counts is a common processing step in 'omic data. We will revisit this after we have @@ -224,6 +230,12 @@ These are a subset of cell surface proteins that show a significant difference between at least two of twelve cell subtypes. That is, all of these genes are either high or low. +[^2]: This a result of the [Central limit + theorem](https://en.wikipedia.org/wiki/Central_limit_theorem),one + consequence of which is that adding together lots of distributions - + whatever distributions they are - will tend to a normal + distribution. + ### Distribution of values across the sample/cells #### 🐸 Frog samples @@ -328,11 +340,11 @@ s30_summary_samp <- s30 |> We can write to file using `write_csv()` -🎬 Write `s30_summary_samp` to a file called -"s30_summary_samp.csv": +🎬 Write `s30_summary_samp` to a file called "s30_summary_samp.csv": ```{r} -write_csv(s30_summary_samp, file = "data-processed/s30_summary_samp.csv") +write_csv(s30_summary_samp, + file = "data-processed/s30_summary_samp.csv") ``` Plotting the distribution of values is perhaps the easiest way to @@ -454,7 +466,7 @@ standard deviation. 🎬 View the `hspc_summary_samp` dataframe (click on it in the environment). -All cells have quite a few zeros and the lower quartile is 0 for al +All cells have quite a few zeros and the lower quartile is 0 for all cells, *i.e.*, every cell has many genes with zero expression. To get a better understanding of the distribution of expressions in @@ -503,7 +515,8 @@ hspc_summary_samp |> ```{r} #| echo: false -write_csv(hspc_summary_samp, file = "data-processed/hspc_summary_samp.csv") +write_csv(hspc_summary_samp, + file = "data-processed/hspc_summary_samp.csv") ``` ### Distribution of values across the genes @@ -581,7 +594,8 @@ counts from 260 to 426) which is exactly what we would expect to see. ```{r} #| echo: false -write_csv(s30_summary_gene, file = "data-processed/s30_summary_gene.csv") +write_csv(s30_summary_gene, + file = "data-processed/s30_summary_gene.csv") ``` #### 🐭 Mouse genes @@ -629,7 +643,7 @@ values but ordering the genes will help. ```{r} hspc_summary_gene |> - ggplot(aes(x = reorder(ensembl_gene_id, mean), y = mean))+ + ggplot(aes(x = reorder(ensembl_gene_id, mean), y = mean)) + geom_pointrange(aes(ymin = mean - sd, ymax = mean + sd), size = 0.1) @@ -643,7 +657,8 @@ expression from1.46 to 3.18) which is expected. ```{r} #| echo: false -write_csv(hspc_summary_gene, file = "data-processed/hspc_summary_gene.csv") +write_csv(hspc_summary_gene, + file = "data-processed/hspc_summary_gene.csv") ``` ## Filtering for QC @@ -656,15 +671,19 @@ values are so low in for a gene that they are uninformative. We will filter the `s30_summary_gene` dataframe to obtain a list of `xenbase_gene_id` we can use to filter `s30`. -My suggestion is to include only the genes with counts in all 6 or 5 out -of 6 samples and those with total counts above 20. +My suggestion is to include only the genes with counts in at least 3 +samples[^3] and those with total counts above 20. + +[^3]: I chose three because that would keep \[0, 0, 0\] \[#,#,#\]. This + is difference we cannot test statistically, but which would matter + biologically. 🎬 Filter the summary by gene dataframe: ```{r} s30_summary_gene_filtered <- s30_summary_gene |> filter(total > 20) |> - filter(n_zero < 2) + filter(n_zero < 4) ``` 🎬 Write the filtered summary by gene to file: @@ -691,7 +710,7 @@ write_csv(s30_filtered, ### 🐭 Mouse filtering -I would take a different approach to filtering the single cell data. For +We will take a different approach to filtering the single cell data. For the Frog samples we are examining the control and the FGF treated samples. This means have a low number of counts overall means the gene is not really expressed (detected) in any condition, and filtering out @@ -736,6 +755,12 @@ improve your comments where your understanding has developed since you made them. Make sure you can close down RStudio, reopen it and run your whole script again. +### πŸ‚ xxxx and future you + +🎬 Create a new Project, `xxxx-88H`, populated with folders and your +data. Make a script file called `xxxx.R`. This will a be commented +analysis of t xxxxxxxxxxxx. + # πŸ₯³ Finished Well Done! @@ -761,15 +786,3 @@ Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr], `kableExtra` [@kableExtra] # References - -[^1]: This a result of the [Central limit - theorem](https://en.wikipedia.org/wiki/Central_limit_theorem),one - consequence of which is that adding together lots of distributions - - whatever distributions they are - will tend to a normal - distribution. - -[^2]: This a result of the [Central limit - theorem](https://en.wikipedia.org/wiki/Central_limit_theorem),one - consequence of which is that adding together lots of distributions - - whatever distributions they are - will tend to a normal - distribution. diff --git a/update-notes.txt b/update-notes.txt index c4a6289..0417ddb 100644 --- a/update-notes.txt +++ b/update-notes.txt @@ -33,3 +33,17 @@ Structure (Michael Plevin) +omics hello data + +usethis::create_project("undergrad-teaching-york/BIO00088H/hello-data") +usethis::use_r("workshop-1") +fs::dir_create("data-raw") +fs::dir_create("data-processed") + + +for workshop 2, make sure you examine which frog genes are 0 in all of one sample but present in all of the other + +which genes matters: first do venn diagram, present absent +then to differential expressions + +