diff --git a/omics/data/betsy/meta_data.txt b/omics/data/betsy/meta_data.txt deleted file mode 100644 index fb451e7..0000000 --- a/omics/data/betsy/meta_data.txt +++ /dev/null @@ -1,19 +0,0 @@ -sample_id stage treatment sibling_rep -S14_C_5 stage_14 control five -S14_C_6 stage_14 control six -S14_C_A stage_14 control A -S14_F_5 stage_14 FGF five -S14_F_6 stage_14 FGF six -S14_F_A stage_14 FGF A -S20_C_5 stage_20 control five -S20_C_6 stage_20 control six -S20_C_A stage_20 control A -S20_F_5 stage_20 FGF five -S20_F_6 stage_20 FGF six -S20_F_A stage_20 FGF A -S30_C_5 stage_30 control five -S30_C_6 stage_30 control six -S30_C_A stage_30 control A -S30_F_5 stage_30 FGF five -S30_F_6 stage_30 FGF six -S30_F_A stage_30 FGF A diff --git a/omics/omics.html b/omics/omics.html index 6057230..3443d78 100644 --- a/omics/omics.html +++ b/omics/omics.html @@ -129,7 +129,7 @@
  • - Week 3: xx + Week 3: Hello data! @@ -165,7 +165,7 @@
  • - Week 4: xxx + Week 4: Statistical Analysis @@ -201,7 +201,7 @@
  • - Week 5: xxx + Week 5: Visualising and Interpreting diff --git a/omics/week-3/data-raw/surfaceome_hspc.csv b/omics/week-3/data-raw/surfaceome_hspc.csv new file mode 100644 index 0000000..080c765 --- /dev/null +++ b/omics/week-3/data-raw/surfaceome_hspc.csv @@ -0,0 +1,281 @@ 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diff --git a/omics/week-3/data-raw/surfaceome_lthsc.csv b/omics/week-3/data-raw/surfaceome_lthsc.csv new file mode 100644 index 0000000..460a05b --- /dev/null +++ b/omics/week-3/data-raw/surfaceome_lthsc.csv @@ -0,0 +1,281 @@ 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  • - Week 3: xx + Week 3: Hello data! @@ -165,7 +165,7 @@
  • - Week 4: xxx + Week 4: Statistical Analysis @@ -201,7 +201,7 @@
  • - Week 5: xxx + Week 5: Visualising and Interpreting diff --git a/omics/week-3/study_after_workshop.html b/omics/week-3/study_after_workshop.html index 6a4eb1c..6fe31dd 100644 --- a/omics/week-3/study_after_workshop.html +++ b/omics/week-3/study_after_workshop.html @@ -140,7 +140,7 @@ - +
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  • - Week 3: xx + Week 3: Hello data! @@ -218,7 +218,7 @@
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    On this page

    • -
  • Getting started
  • Exercises
    • @@ -345,187 +340,72 @@

    Introduction

    Session overview

    In this workshop you will

    -
    -
    -
    - -
    -
    -Key -
    -
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    - -
    -
    -
    - -
    -

    Getting started

    -
    -
    library(tidyverse)
    -
    -
    tidyverse_conflicts() ──
-✖ dplyr::filter() masks stats::filter()
-✖ dplyr::lag()    masks stats::lag()
-ℹ Use the conflicted package to force all conflicts to become errors

    See later workshops.

    +

    Exercises

    Set up a Project

    -
    -
    -

    Examine your data

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    -

    Meta data

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    Frog development: meta_data.txt

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    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    sample_idstagetreatmentsibling_rep
    S14_C_5stage_14controlfive
    S14_C_6stage_14controlsix
    S14_C_Astage_14controlA
    S14_F_5stage_14FGFfive
    S14_F_6stage_14FGFsix
    S14_F_Astage_14FGFA
    S20_C_5stage_20controlfive
    S20_C_6stage_20controlsix
    S20_C_Astage_20controlA
    S20_F_5stage_20FGFfive
    S20_F_6stage_20FGFsix
    S20_F_Astage_20FGFA
    S30_C_5stage_30controlfive
    S30_C_6stage_30controlsix
    S30_C_Astage_30controlA
    S30_F_5stage_30FGFfive
    S30_F_6stage_30FGFsix
    S30_F_Astage_30FGFA
    -
    +
    library(tidyverse)
    -
    -

    Data

    +
    +

    Examine your data

    +

    The workshops will examine the “least interesting”: - the difference between the control and the FGF treated sibling at S30 - the difference between HSPC and Prog cells

    +

    🐸 Frog development data - xlaevis_counts_S14.csv - xlaevis_counts_S20.csv - xlaevis_counts_S30.csv - meta_data.txt

    +

    🐭 Stem cell data - surfaceome_hspc.csv - surfaceome_prog.csv - surfaceome_lthsc.csv

      -
    • open in understanding the data numbers of variables, organisation
      • +
    • 🎬 Save the files to data-raw
      • +
    • 🎬 Open the data files in Excel
      • +
    • 🎬 Describe what is in the rows and columns of each file.
      • +
    • 🎬 How many rows and columns are there in each file? Are these the same? In all cases or some cases? Why?
      • +
    • 🎬 Google an id. Where does your search take you? How much information is available?
      • +
    • 🎬 Did you record all that??
    -

    Import

    + +
    +
    # 🐸 import the s30 data
+s30 <- read_csv("data-raw/xlaevis_counts_S30.csv")
    +
    +
    +
    # 🐭 import the hspc data
+hspc <- read_csv("data-raw/surfaceome_hspc.csv")
    +
    +
    +
    # 🐭 import the progs data
+prog <- read_csv("data-raw/surfaceome_prog.csv")
    +
    +
      +
    • 🎬 Check these have the number of rows and column you were expecting and that column types and names are as expected.
      • +

    Explore

    +

    The

    +

    Distributions

    • what kind of values are they, how many missing
    • qc plots
    • removing the useless, writing to files
    +

    🐸 Frog development data - 🎬 Make a script file called cont-fgf-s30.R. This will a be commented analysis of the control vs FGF at S30 comparison. You will build on this each workshop and be able to use it as a template to examine other comparisons. Copy in the appropriate code and comments from workshop-1.R. Edit to improve your comments where your understanding has developed since you made them.

    +

    🐭 Stem cell data - 🎬 Save the files to data-raw

    🎬

    You’re finished!

    diff --git a/search.json b/search.json index f53a61b..4b62a5d 100644 --- a/search.json +++ b/search.json @@ -179,42 +179,42 @@ "href": "omics/week-3/workshop.html", "title": "Workshop", "section": "", - "text": "In this workshop you will\n\n\n\n\n\n\nKey" + "text": "In this workshop you will\nSee later workshops." }, { "objectID": "omics/week-3/workshop.html#session-overview", "href": "omics/week-3/workshop.html#session-overview", "title": "Workshop", "section": "", - "text": "In this workshop you will\n\n\n\n\n\n\nKey" + "text": "In this workshop you will\nSee later workshops." }, { "objectID": "omics/week-3/workshop.html#set-up-a-project", "href": "omics/week-3/workshop.html#set-up-a-project", "title": "Workshop", "section": "Set up a Project", - "text": "Set up a Project\n\nset up a project and create the organisation" + "text": "Set up a Project\n\n🎬 Start RStudio from the Start menu\n🎬 Make an RStudio project. Be deliberate about where you create it so that it is a good place for you\n🎬 Use the Files pane to make a new folder for the data. I suggest data-raw\n🎬 Make a new script called workshop-1.R to carry out the rest of the work.\n🎬 Record what you do and what you find out. All of it!\n🎬 Load tidyverse\n\n\nlibrary(tidyverse)" }, { "objectID": "omics/week-3/workshop.html#examine-your-data", "href": "omics/week-3/workshop.html#examine-your-data", "title": "Workshop", "section": "Examine your data", - "text": "Examine your data\n\nMeta data\nFrog development: meta_data.txt\n\n\n\n\n\nsample_id\nstage\ntreatment\nsibling_rep\n\n\n\n\nS14_C_5\nstage_14\ncontrol\nfive\n\n\nS14_C_6\nstage_14\ncontrol\nsix\n\n\nS14_C_A\nstage_14\ncontrol\nA\n\n\nS14_F_5\nstage_14\nFGF\nfive\n\n\nS14_F_6\nstage_14\nFGF\nsix\n\n\nS14_F_A\nstage_14\nFGF\nA\n\n\nS20_C_5\nstage_20\ncontrol\nfive\n\n\nS20_C_6\nstage_20\ncontrol\nsix\n\n\nS20_C_A\nstage_20\ncontrol\nA\n\n\nS20_F_5\nstage_20\nFGF\nfive\n\n\nS20_F_6\nstage_20\nFGF\nsix\n\n\nS20_F_A\nstage_20\nFGF\nA\n\n\nS30_C_5\nstage_30\ncontrol\nfive\n\n\nS30_C_6\nstage_30\ncontrol\nsix\n\n\nS30_C_A\nstage_30\ncontrol\nA\n\n\nS30_F_5\nstage_30\nFGF\nfive\n\n\nS30_F_6\nstage_30\nFGF\nsix\n\n\nS30_F_A\nstage_30\nFGF\nA\n\n\n\n\n\n\n\nData\n\nopen in understanding the data numbers of variables, organisation" + "text": "Examine your data\nThe workshops will examine the “least interesting”: - the difference between the control and the FGF treated sibling at S30 - the difference between HSPC and Prog cells\n🐸 Frog development data - xlaevis_counts_S14.csv - xlaevis_counts_S20.csv - xlaevis_counts_S30.csv - meta_data.txt\n🐭 Stem cell data - surfaceome_hspc.csv - surfaceome_prog.csv - surfaceome_lthsc.csv\n\n🎬 Save the files to data-raw\n🎬 Open the data files in Excel\n🎬 Describe what is in the rows and columns of each file.\n🎬 How many rows and columns are there in each file? Are these the same? In all cases or some cases? Why?\n🎬 Google an id. Where does your search take you? How much information is available?\n🎬 Did you record all that??" }, { "objectID": "omics/week-3/workshop.html#import", "href": "omics/week-3/workshop.html#import", "title": "Workshop", "section": "Import", - "text": "Import" + "text": "Import\n\nopen in understanding the data numbers of variables, organisation\n🎬 Import xlaevis_counts_S30.csv, surfaceome_hspc.csv and surfaceome_prog.csv\n\n\n# 🐸 import the s30 data\ns30 <- read_csv(\"data-raw/xlaevis_counts_S30.csv\")\n\n\n# 🐭 import the hspc data\nhspc <- read_csv(\"data-raw/surfaceome_hspc.csv\")\n\n\n# 🐭 import the progs data\nprog <- read_csv(\"data-raw/surfaceome_prog.csv\")\n\n\n🎬 Check these have the number of rows and column you were expecting and that column types and names are as expected." }, { "objectID": "omics/week-3/workshop.html#explore", "href": "omics/week-3/workshop.html#explore", "title": "Workshop", "section": "Explore", - "text": "Explore\n\nwhat kind of values are they, how many missing\nqc plots\nremoving the useless, writing to files\n\n🎬\nYou’re finished!" + "text": "Explore\nThe\nDistributions\n\nwhat kind of values are they, how many missing\nqc plots\nremoving the useless, writing to files\n\n🐸 Frog development data - 🎬 Make a script file called cont-fgf-s30.R. This will a be commented analysis of the control vs FGF at S30 comparison. You will build on this each workshop and be able to use it as a template to examine other comparisons. Copy in the appropriate code and comments from workshop-1.R. Edit to improve your comments where your understanding has developed since you made them.\n🐭 Stem cell data - 🎬 Save the files to data-raw\n🎬\nYou’re finished!" }, { "objectID": "omics/week-3/study_before_workshop.html#sequence-data",