The goal of scitargets is to help you analyse single-cell CITE-seq data by providing target factories and parametized report to deal with basic quality controls, HTO demultiplexing, and celltypes annotation.
You can install scitargets using devtools. Keep the build_vignettes argument to get the package documentation:
install.package("devtools")
# At the time I write this, seurat is on the version 5.3.0 on cran.
# I force seurat 5.3.1 or higher as the 5.3.0 version is bugged when using the azimuth package
devtools::install_github("satijalab/seurat", "fix/v.5.3.1", force=TRUE)
devtools::install_github("https://github.com/Pierre9344/scitargets", build_vignettes = T)
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In Rstudio, create a new project using scitargets project template (File -> New Project -> New Directory -> Project template for scitargets).
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Copy your cellranger output inside "data/cellranger_output/" folder. Create a subfolder for each run.
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Open the "_targets.R" script and modify it to run the pipeline on each run.
- Duplicate the "tar_demultiplex_hto" function to have one call per run and modify the argument (the run_id argument must correspond the subfolder in "data/cellranger_output/".
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(Optional), unquote the "crew" code in "_targets.R" to allow a parallelization of the pipeline steps and accelerate the pipeline).
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Duplicate the ".qmd" reports (QMD folder) so that you have one document per run.
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Modify the document to fit your run:
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set the RUN_ID parameter (inside the yaml header) to the name of the run folder inside the data/cellranger_output/ folder.
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replace all occurence of "RUN_ID" by "<your_run_id>" (same as the RUN_ID parameter in the yaml header).
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Modify the "_quarto.yml" file to indicate each reports (qmd document) inside the website
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Run the pipeline using "targets::tar_make()"
library(targets)
tar_make()
Check the vignettes for more details.
Build-in Azimuth annotation are currently only available for the (human) pbmc-ref of the SeuratData package.
It is also recommanded to use:
- Seurat 5.3.1.1000
- SeuratObject 5.2.0
- Azimuth 0.5.0
Other versions may be compatible but not tested