Last updated: 2021-11-08
Checks: 7 0
Knit directory: svi-rmit_scrna-seq-workshop_2021-november/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20190102) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version cd0f9f4. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Untracked files:
Untracked: svi-rmit_scrna-seq-workshop_2021-november.Rproj
Untracked: untar_path/
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (public/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | cd0f9f4 | Davis McCarthy | 2021-11-08 | Updating for SVI-RMIT workshop |
| html | 4bc9139 | Davis McCarthy | 2021-07-07 | Updated web pages |
| Rmd | d13d36f | Davis McCarthy | 2021-07-07 | Updating workshop content |
| html | 9ec2636 | Davis McCarthy | 2021-07-05 | Substantial updates to workflow |
| Rmd | c5ce76b | Davis McCarthy | 2021-07-05 | Fixed a typo |
| Rmd | 2751b16 | Davis McCarthy | 2021-07-05 | Minor tweak to intro |
| html | 752aaa3 | Davis McCarthy | 2021-07-05 | Updating workflowr website |
| html | 15804b7 | Davis McCarthy | 2021-07-01 | Checking in edits |
| Rmd | a63decb | Davis McCarthy | 2021-06-29 | Minor tweaks |
| html | bcc60d6 | Davis McCarthy | 2021-06-29 | Updated html pages |
| Rmd | ed221af | Davis McCarthy | 2021-06-29 | Tweaks to workflowr pages |
| html | ed221af | Davis McCarthy | 2021-06-29 | Tweaks to workflowr pages |
| Rmd | 8cdfd4d | Davis McCarthy | 2021-06-29 | Updating materials for workshop in July 2021 |
| html | 8cdfd4d | Davis McCarthy | 2021-06-29 | Updating materials for workshop in July 2021 |
In this workshop, we will introduce the data infrastructure for scRNA-seq analysis in R and practice a workflow of scRNAseq analysis; from pre-processing, quality control to dimensionality reduction and clustering, marker gene detection and cell type annotation - with plenty more along the way!
We use the Bioconductor single-cell ecosystem for this workshop. Thus, participants will need a recent version of R (version 4.0+) and a set of specific packages that we use.
The code snippet below will install the necessary packages for you in R (i.e. run the following code at the R prompt in an R or RStudio session). The first line installs the BiocManager package, which is the preferred package for then installing Bioconductor packages. The next (long) line then installs the necessary Bioconductor packages (and any dependencies).
install.packages("BiocManager")
BiocManager::install(c("scRNAseq",
"scater",
"scran",
"clustree",
"BiocSingular",
"Rtsne",
"BiocFileCache",
"DropletUtils",
"EnsDb.Hsapiens.v86",
"schex",
"celldex",
"SingleR",
"gridExtra"))If you have trouble with the package installation, please ask a colleague for help.
Once you have installed the packages, you’re ready to go with the workshop. So let’s…
Follow this link for the single-cell RNA-seq analysis workflow focusing on cell type identification.
devtools::session_info()─ Session info 🛫 🖕🏽 🔩 ─────────────────────────────────────────────────
hash: airplane departure, middle finger: medium skin tone, nut and bolt
setting value
version R version 4.1.1 (2021-08-10)
os macOS Big Sur 10.16
system x86_64, darwin17.0
ui X11
language (EN)
collate en_AU.UTF-8
ctype en_AU.UTF-8
tz Australia/Melbourne
date 2021-11-08
pandoc 2.11.4 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
bslib 0.3.1 2021-10-06 [1] CRAN (R 4.1.0)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.0)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0)
cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.0)
crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.0)
desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.0)
devtools 2.4.2 2021-06-07 [1] CRAN (R 4.1.0)
digest 0.6.28 2021-09-23 [1] CRAN (R 4.1.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0)
git2r 0.28.0 2021-01-10 [1] CRAN (R 4.1.0)
glue 1.5.0 2021-11-07 [1] CRAN (R 4.1.1)
htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.0)
httpuv 1.6.3 2021-09-09 [1] CRAN (R 4.1.0)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.1.0)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.0)
knitr 1.36 2021-09-29 [1] CRAN (R 4.1.0)
later 1.3.0 2021-08-18 [1] CRAN (R 4.1.0)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.0)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.1.0)
pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.0)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
pkgload 1.2.3 2021-10-13 [1] CRAN (R 4.1.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.0)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.1.0)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0)
Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.0)
remotes 2.4.1 2021-09-29 [1] CRAN (R 4.1.0)
rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.0)
rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.1)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
sass 0.4.0 2021-05-12 [1] CRAN (R 4.1.0)
sessioninfo 1.2.1 2021-11-02 [1] CRAN (R 4.1.0)
stringi 1.7.5 2021-10-04 [1] CRAN (R 4.1.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
testthat 3.1.0 2021-10-04 [1] CRAN (R 4.1.0)
tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.1)
usethis 2.1.3 2021-10-27 [1] CRAN (R 4.1.0)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0)
whisker 0.4 2019-08-28 [1] CRAN (R 4.1.0)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.0)
workflowr 1.6.2 2020-04-30 [1] CRAN (R 4.1.0)
xfun 0.28 2021-11-04 [1] CRAN (R 4.1.1)
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0)
[1] /Users/dmccarthy/Library/R/x86_64/4.1/library
[2] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
──────────────────────────────────────────────────────────────────────────────