usethis::create_project("bananas")usethis::create_project("bananas")🎬 The example RStudio project containing this code here: chaffinch. You can download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project. You may want to navigate to a particular directory or edit the destdir:
usethis::use_course(url = "3mmaRand/chaffinch", destdir = ".")usethis::use_course(url = "3mmaRand/chaffinch", destdir = ".")You can agree to deleting the zip. You should find RStudio restarts and you have a new project called chaffinch-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repo you downloaded. You can now run the code in the project.
🎬 Make an outline of your compendium. This could be a sketch on paper or slide or from the mindmap software you usually use. Or it could be a skeleton of folders and files on your computer.
🎬 Make a start on a quarto doc.
diff --git a/core/week-2/study_before_workshop.html b/core/week-2/study_before_workshop.html index 3e519b9..1833937 100644 --- a/core/week-2/study_before_workshop.html +++ b/core/week-2/study_before_workshop.html @@ -576,13 +576,13 @@If this is a good place to create a Project directory then…
🎬 Create a project with:
usethis::create_project("bananas")usethis::create_project("bananas")usethis packageOtherwise
If you want the project directory elsewhere, you will need to give the relative path, e.g.
usethis::create_project("../Documents/bananas")usethis::create_project("../Documents/bananas")usethis packageThe output will look like this and a new RStudio session will start.
@@ -639,7 +639,7 @@🎬 We can add a README with:
usethis::use_readme_md()usethis::use_readme_md()total 128
-drwxr-xr-x 2 runner docker 4096 Mar 28 13:59 data
-drwxr-xr-x 2 runner docker 4096 Mar 28 13:59 images
--rw-r--r-- 1 runner docker 1597 Mar 28 13:59 overview.qmd
--rw-r--r-- 1 runner docker 184 Mar 28 13:59 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4807 Mar 28 13:59 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Mar 28 13:59 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 58063 Mar 28 13:59 workshop.html
--rw-r--r-- 1 runner docker 8550 Mar 28 13:59 workshop.qmd
--rw-r--r-- 1 runner docker 8564 Mar 28 14:23 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4096 Mar 28 13:59 workshop_filesYou 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:
total 128K
-drwxr-xr-x 2 runner docker 4.0K Mar 28 13:59 data
-drwxr-xr-x 2 runner docker 4.0K Mar 28 13:59 images
--rw-r--r-- 1 runner docker 1.6K Mar 28 13:59 overview.qmd
--rw-r--r-- 1 runner docker 184 Mar 28 13:59 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Mar 28 13:59 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13K Mar 28 13:59 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 57K Mar 28 13:59 workshop.html
--rw-r--r-- 1 runner docker 8.4K Mar 28 13:59 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Mar 28 14:23 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Mar 28 13:59 workshop_filesThe -a option stands for “all” and shows us all the files, including hidden files.
total 136K
-drwxr-xr-x 5 runner docker 4.0K Mar 28 14:23 .
-drwxr-xr-x 6 runner docker 4.0K Mar 28 13:59 ..
-drwxr-xr-x 2 runner docker 4.0K Mar 28 13:59 data
-drwxr-xr-x 2 runner docker 4.0K Mar 28 13:59 images
--rw-r--r-- 1 runner docker 1.6K Mar 28 13:59 overview.qmd
--rw-r--r-- 1 runner docker 184 Mar 28 13:59 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Mar 28 13:59 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13K Mar 28 13:59 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 57K Mar 28 13:59 workshop.html
--rw-r--r-- 1 runner docker 8.4K Mar 28 13:59 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Mar 28 14:23 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Mar 28 13:59 workshop_filesYou 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:
You now have a dataframe with all the tracking data which is relatively easy to summarise and plot using tools you know.
There is an example RStudio project containing this code here: tips. You can also download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project. You may want to navigate to a particular directory or edit the destdir:
usethis::use_course(url = "3mmaRand/tips", destdir = ".")usethis::use_course(url = "3mmaRand/tips", destdir = ".")You can agree to deleting the zip. You should find RStudio restarts and you have a new project called tips-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repo you downloaded. You can now run the code in the project.
diff --git a/omics/kelly/workshop.html b/omics/kelly/workshop.html index ee4fd49..db388b5 100644 --- a/omics/kelly/workshop.html +++ b/omics/kelly/workshop.html @@ -1344,8 +1344,8 @@The heatmap will open in the viewer pane (rather than the plot pane) because it is html. You can “Show in a new window” to see it in a larger format. You can also zoom in and out and pan around the heatmap and download it as a png. You might feel the colour bars is not adding much to the plot. You can remove it by setting hide_colorbar = TRUE, in the heatmaply() function.
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.
@@ -1060,8 +1060,8 @@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 e88f219..c5cc85a 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 8bd2d79..01878d4 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 bf27b16..c081a37 100644 --- a/search.json +++ b/search.json @@ -2016,7 +2016,7 @@ "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.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 128\ndrwxr-xr-x 2 runner docker 4096 Mar 28 13:59 data\ndrwxr-xr-x 2 runner docker 4096 Mar 28 13:59 images\n-rw-r--r-- 1 runner docker 1597 Mar 28 13:59 overview.qmd\n-rw-r--r-- 1 runner docker 184 Mar 28 13:59 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4807 Mar 28 13:59 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Mar 28 13:59 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 58063 Mar 28 13:59 workshop.html\n-rw-r--r-- 1 runner docker 8550 Mar 28 13:59 workshop.qmd\n-rw-r--r-- 1 runner docker 8564 Mar 28 14:23 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4096 Mar 28 13:59 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 128K\ndrwxr-xr-x 2 runner docker 4.0K Mar 28 13:59 data\ndrwxr-xr-x 2 runner docker 4.0K Mar 28 13:59 images\n-rw-r--r-- 1 runner docker 1.6K Mar 28 13:59 overview.qmd\n-rw-r--r-- 1 runner docker 184 Mar 28 13:59 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Mar 28 13:59 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Mar 28 13:59 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 57K Mar 28 13:59 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Mar 28 13:59 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Mar 28 14:23 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Mar 28 13:59 workshop_files\n\n\nThe -a option stands for “all” and shows us all the files, including hidden files.\n\nls -alh\n\ntotal 136K\ndrwxr-xr-x 5 runner docker 4.0K Mar 28 14:23 .\ndrwxr-xr-x 6 runner docker 4.0K Mar 28 13:59 ..\ndrwxr-xr-x 2 runner docker 4.0K Mar 28 13:59 data\ndrwxr-xr-x 2 runner docker 4.0K Mar 28 13:59 images\n-rw-r--r-- 1 runner docker 1.6K Mar 28 13:59 overview.qmd\n-rw-r--r-- 1 runner docker 184 Mar 28 13:59 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Mar 28 13:59 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Mar 28 13:59 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 57K Mar 28 13:59 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Mar 28 13:59 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Mar 28 14:23 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Mar 28 13:59 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.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 128\ndrwxr-xr-x 2 runner docker 4096 Mar 28 17:29 data\ndrwxr-xr-x 2 runner docker 4096 Mar 28 17:29 images\n-rw-r--r-- 1 runner docker 1597 Mar 28 17:29 overview.qmd\n-rw-r--r-- 1 runner docker 184 Mar 28 17:29 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4807 Mar 28 17:29 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Mar 28 17:29 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 58063 Mar 28 17:29 workshop.html\n-rw-r--r-- 1 runner docker 8550 Mar 28 17:29 workshop.qmd\n-rw-r--r-- 1 runner docker 8564 Mar 28 17:32 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4096 Mar 28 17:29 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 128K\ndrwxr-xr-x 2 runner docker 4.0K Mar 28 17:29 data\ndrwxr-xr-x 2 runner docker 4.0K Mar 28 17:29 images\n-rw-r--r-- 1 runner docker 1.6K Mar 28 17:29 overview.qmd\n-rw-r--r-- 1 runner docker 184 Mar 28 17:29 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Mar 28 17:29 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Mar 28 17:29 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 57K Mar 28 17:29 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Mar 28 17:29 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Mar 28 17:32 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Mar 28 17:29 workshop_files\n\n\nThe -a option stands for “all” and shows us all the files, including hidden files.\n\nls -alh\n\ntotal 136K\ndrwxr-xr-x 5 runner docker 4.0K Mar 28 17:32 .\ndrwxr-xr-x 6 runner docker 4.0K Mar 28 17:29 ..\ndrwxr-xr-x 2 runner docker 4.0K Mar 28 17:29 data\ndrwxr-xr-x 2 runner docker 4.0K Mar 28 17:29 images\n-rw-r--r-- 1 runner docker 1.6K Mar 28 17:29 overview.qmd\n-rw-r--r-- 1 runner docker 184 Mar 28 17:29 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Mar 28 17:29 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Mar 28 17:29 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 57K Mar 28 17:29 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Mar 28 17:29 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Mar 28 17:32 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Mar 28 17:29 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", "crumbs": [ "Core", "Week 2: Workflow tips", diff --git a/structures/structures.html b/structures/structures.html index 1bbc784..4641026 100644 --- a/structures/structures.html +++ b/structures/structures.html @@ -258,7 +258,7 @@I think that’s it! You can now download the RStudio project and run each chunk in the quarto document.
There is an example RStudio project here: structure-analysis. You can also download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project. You may want to navigate to a particular directory or edit the destdir:
usethis::use_course(url = "3mmaRand/structure-analysis", destdir = ".")usethis::use_course(url = "3mmaRand/structure-analysis", destdir = ".")You can agree to deleting the zip. You should find RStudio restarts and you have a new project called structure-analysis-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repo you downloaded.
You should be able to open the antibody_mimetics_workshop_3.qmd file and run each chunk. You can also knit the document to html.