On the vertical axis are genes which are differentially expressed at the 0.01 level. On the horizontal axis are samples. We can see that the FGF-treated samples cluster together and the control samples cluster together. We can also see two clusters of genes; one of these shows genes upregulated (more yellow) in the FGF-treated samples (the pink cluster) and the other shows genes down regulated (more blue, the blue cluster) in the FGF-treated samples.
@@ -1014,8 +1014,8 @@It will take a minute to run and display. On the vertical axis are genes which are differentially expressed at the 0.01 level. On the horizontal axis are cells. We can see that cells of the same type don’t cluster that well together. We can also see two clusters of genes but the pattern of gene is not as clear as it was for the frogs and the correspondence with the cell clusters is not as strong.
diff --git a/omics/week-5/workshop_files/figure-html/unnamed-chunk-33-1.png b/omics/week-5/workshop_files/figure-html/unnamed-chunk-33-1.png index 5116318..c4e2dca 100644 Binary files a/omics/week-5/workshop_files/figure-html/unnamed-chunk-33-1.png and b/omics/week-5/workshop_files/figure-html/unnamed-chunk-33-1.png differ diff --git a/omics/week-5/workshop_files/figure-html/unnamed-chunk-65-1.png b/omics/week-5/workshop_files/figure-html/unnamed-chunk-65-1.png index aea2acd..516dbd8 100644 Binary files a/omics/week-5/workshop_files/figure-html/unnamed-chunk-65-1.png and b/omics/week-5/workshop_files/figure-html/unnamed-chunk-65-1.png differ diff --git a/search.json b/search.json index 8ce1b9c..a22b5e6 100644 --- a/search.json +++ b/search.json @@ -886,7 +886,7 @@ "href": "core/week-2/workshop.html#rstudio-terminal", "title": "Workshop", "section": "RStudio terminal", - "text": "RStudio terminal\nThe RStudio terminal is a convenient interface to the shell without leaving RStudio. It is useful for running commands that are not available in R. For example, you can use it to run other programs like fasqc, git, ftp, ssh\nNavigating your file system\nSeveral commands are frequently used to create, inspect, rename, and delete files and directories.\n$\nThe dollar sign is the prompt (like > on the R console), which shows us that the shell is waiting for input.\nYou can find out where you are using the pwd command, which stands for “print working directory”.\n\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2\n\n\nYou can find out what you can see with ls which stands for “list”.\n\nls\n\ndata\nimages\noverview.html\noverview.qmd\nstudy_after_workshop.qmd\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.html\nworkshop.qmd\nworkshop.rmarkdown\nworkshop_files\n\n\nYou might have noticed that unlike R, the commands do not have brackets after them. Instead, options (or switches) are given after the command. For example, we can modify the ls command to give us more information with the -l option, which stands for “long”.\n\nls -l\n\ntotal 140\ndrwxr-xr-x 2 runner docker 4096 Nov 9 17:24 data\ndrwxr-xr-x 2 runner docker 4096 Nov 9 17:24 images\n-rw-r--r-- 1 runner docker 27168 Nov 9 17:25 overview.html\n-rw-r--r-- 1 runner docker 1597 Nov 9 17:24 overview.qmd\n-rw-r--r-- 1 runner docker 184 Nov 9 17:24 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4807 Nov 9 17:24 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Nov 9 17:24 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 44938 Nov 9 17:24 workshop.html\n-rw-r--r-- 1 runner docker 8550 Nov 9 17:24 workshop.qmd\n-rw-r--r-- 1 runner docker 8564 Nov 9 17:25 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4096 Nov 9 17:24 workshop_files\n\n\nYou can use more than one option at once. The -h option stands for “human readable” and makes the file sizes easier to understand for humans:\n\nls -hl\n\ntotal 140K\ndrwxr-xr-x 2 runner docker 4.0K Nov 9 17:24 data\ndrwxr-xr-x 2 runner docker 4.0K Nov 9 17:24 images\n-rw-r--r-- 1 runner docker 27K Nov 9 17:25 overview.html\n-rw-r--r-- 1 runner docker 1.6K Nov 9 17:24 overview.qmd\n-rw-r--r-- 1 runner docker 184 Nov 9 17:24 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Nov 9 17:24 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Nov 9 17:24 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 44K Nov 9 17:24 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Nov 9 17:24 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Nov 9 17:25 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Nov 9 17:24 workshop_files\n\n\nThe -a option stands for “all” and shows us all the files, including hidden files.\n\nls -alh\n\ntotal 148K\ndrwxr-xr-x 5 runner docker 4.0K Nov 9 17:25 .\ndrwxr-xr-x 6 runner docker 4.0K Nov 9 17:25 ..\ndrwxr-xr-x 2 runner docker 4.0K Nov 9 17:24 data\ndrwxr-xr-x 2 runner docker 4.0K Nov 9 17:24 images\n-rw-r--r-- 1 runner docker 27K Nov 9 17:25 overview.html\n-rw-r--r-- 1 runner docker 1.6K Nov 9 17:24 overview.qmd\n-rw-r--r-- 1 runner docker 184 Nov 9 17:24 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Nov 9 17:24 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Nov 9 17:24 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 44K Nov 9 17:24 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Nov 9 17:24 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Nov 9 17:25 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Nov 9 17:24 workshop_files\n\n\nYou can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:\n\ncd data\npwd\ncd ..\npwd\ncd data\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2/data\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2/data\n\n\nhead 1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nhead -20 data/1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nSOURCE 3 ORGANISM_COMMON: SPERM WHALE; \nSOURCE 4 ORGANISM_TAXID: 9755; \nSOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; \nSOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; \nSOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; \nSOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15A \nKEYWDS HELICAL, GLOBULAR, ALL-HYDROGEN CONTAINING STRUCTURE, OXYGEN STORAGE- \nKEYWDS 2 TRANSPORT COMPLEX \nEXPDTA NEUTRON DIFFRACTION \nAUTHOR F.SHU,V.RAMAKRISHNAN,B.P.SCHOENBORN \nless 1cq2.pdb\nless is a program that displays the contents of a file, one page at a time. It is useful for viewing large files because it does not load the whole file into memory before displaying it. Instead, it reads and displays a few lines at a time. You can navigate forward through the file with the spacebar, and backwards with the b key. Press q to quit.\nA wildcard is a character that can be used as a substitute for any of a class of characters in a search, The most common wildcard characters are the asterisk (*) and the question mark (?).\nls *.csv\ncp stands for “copy”. You can copy a file from one directory to another by giving cp the path to the file you want to copy and the path to the destination directory.\ncp 1cq2.pdb copy_of_1cq2.pdb\ncp 1cq2.pdb ../copy_of_1cq2.pdb\ncp 1cq2.pdb ../bob.txt\nTo delete a file use the rm command, which stands for “remove”.\nrm ../bob.txt\nbut be careful because the file will be gone forever. There is no “are you sure?” or undo.\nTo move a file from one directory to another, use the mv command. mv works like cp except that it also deletes the original file.\nmv ../copy_of_1cq2.pdb .\nMake a directory\nmkdir mynewdir" + "text": "RStudio terminal\nThe RStudio terminal is a convenient interface to the shell without leaving RStudio. It is useful for running commands that are not available in R. For example, you can use it to run other programs like fasqc, git, ftp, ssh\nNavigating your file system\nSeveral commands are frequently used to create, inspect, rename, and delete files and directories.\n$\nThe dollar sign is the prompt (like > on the R console), which shows us that the shell is waiting for input.\nYou can find out where you are using the pwd command, which stands for “print working directory”.\n\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2\n\n\nYou can find out what you can see with ls which stands for “list”.\n\nls\n\ndata\nimages\noverview.html\noverview.qmd\nstudy_after_workshop.qmd\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.html\nworkshop.qmd\nworkshop.rmarkdown\nworkshop_files\n\n\nYou might have noticed that unlike R, the commands do not have brackets after them. Instead, options (or switches) are given after the command. For example, we can modify the ls command to give us more information with the -l option, which stands for “long”.\n\nls -l\n\ntotal 140\ndrwxr-xr-x 2 runner docker 4096 Nov 20 08:50 data\ndrwxr-xr-x 2 runner docker 4096 Nov 20 08:50 images\n-rw-r--r-- 1 runner docker 27167 Nov 20 09:12 overview.html\n-rw-r--r-- 1 runner docker 1597 Nov 20 08:50 overview.qmd\n-rw-r--r-- 1 runner docker 184 Nov 20 08:50 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4807 Nov 20 08:50 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Nov 20 08:50 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 44938 Nov 20 08:50 workshop.html\n-rw-r--r-- 1 runner docker 8550 Nov 20 08:50 workshop.qmd\n-rw-r--r-- 1 runner docker 8564 Nov 20 09:12 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4096 Nov 20 08:50 workshop_files\n\n\nYou can use more than one option at once. The -h option stands for “human readable” and makes the file sizes easier to understand for humans:\n\nls -hl\n\ntotal 140K\ndrwxr-xr-x 2 runner docker 4.0K Nov 20 08:50 data\ndrwxr-xr-x 2 runner docker 4.0K Nov 20 08:50 images\n-rw-r--r-- 1 runner docker 27K Nov 20 09:12 overview.html\n-rw-r--r-- 1 runner docker 1.6K Nov 20 08:50 overview.qmd\n-rw-r--r-- 1 runner docker 184 Nov 20 08:50 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Nov 20 08:50 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Nov 20 08:50 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 44K Nov 20 08:50 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Nov 20 08:50 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Nov 20 09:12 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Nov 20 08:50 workshop_files\n\n\nThe -a option stands for “all” and shows us all the files, including hidden files.\n\nls -alh\n\ntotal 148K\ndrwxr-xr-x 5 runner docker 4.0K Nov 20 09:12 .\ndrwxr-xr-x 6 runner docker 4.0K Nov 20 09:12 ..\ndrwxr-xr-x 2 runner docker 4.0K Nov 20 08:50 data\ndrwxr-xr-x 2 runner docker 4.0K Nov 20 08:50 images\n-rw-r--r-- 1 runner docker 27K Nov 20 09:12 overview.html\n-rw-r--r-- 1 runner docker 1.6K Nov 20 08:50 overview.qmd\n-rw-r--r-- 1 runner docker 184 Nov 20 08:50 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Nov 20 08:50 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Nov 20 08:50 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 44K Nov 20 08:50 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Nov 20 08:50 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Nov 20 09:12 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Nov 20 08:50 workshop_files\n\n\nYou can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:\n\ncd data\npwd\ncd ..\npwd\ncd data\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2/data\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2/data\n\n\nhead 1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nhead -20 data/1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nSOURCE 3 ORGANISM_COMMON: SPERM WHALE; \nSOURCE 4 ORGANISM_TAXID: 9755; \nSOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; \nSOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; \nSOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; \nSOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15A \nKEYWDS HELICAL, GLOBULAR, ALL-HYDROGEN CONTAINING STRUCTURE, OXYGEN STORAGE- \nKEYWDS 2 TRANSPORT COMPLEX \nEXPDTA NEUTRON DIFFRACTION \nAUTHOR F.SHU,V.RAMAKRISHNAN,B.P.SCHOENBORN \nless 1cq2.pdb\nless is a program that displays the contents of a file, one page at a time. It is useful for viewing large files because it does not load the whole file into memory before displaying it. Instead, it reads and displays a few lines at a time. You can navigate forward through the file with the spacebar, and backwards with the b key. Press q to quit.\nA wildcard is a character that can be used as a substitute for any of a class of characters in a search, The most common wildcard characters are the asterisk (*) and the question mark (?).\nls *.csv\ncp stands for “copy”. You can copy a file from one directory to another by giving cp the path to the file you want to copy and the path to the destination directory.\ncp 1cq2.pdb copy_of_1cq2.pdb\ncp 1cq2.pdb ../copy_of_1cq2.pdb\ncp 1cq2.pdb ../bob.txt\nTo delete a file use the rm command, which stands for “remove”.\nrm ../bob.txt\nbut be careful because the file will be gone forever. There is no “are you sure?” or undo.\nTo move a file from one directory to another, use the mv command. mv works like cp except that it also deletes the original file.\nmv ../copy_of_1cq2.pdb .\nMake a directory\nmkdir mynewdir" }, { "objectID": "core/week-2/workshop.html#differences-between-r-and-python",