A repository that contains files for processing scRNA-seq seurat objects.
QBStanAnn.Rmd is the main Rmarkdown that calls the QC, Annotation, and Differential Expression scripts.
QCSStan.RMD is the quality control (QC) and standardization (S) file in which that seurat object is normalized, scaled, and cleared of dead cells and doublets.
Ann.Rmd is a general script to perform cell type annotation of single cell RNA-seq datasets.
DEx.Rmd identifies differential expressed genes in scRNA-seq data.
QB_SingleCell_quickpass.Rmd is a file for quick processing and QC of new data sets. Because this script downsamples the cells, it should run in about 15-20 minutes.
- support for mouse and human
- doublet detection and filtering (via scds)
- decontamination detection and filtering (via DecontX)
- multiple filtering options (including hard filters and MAD)
- standard or SCT transformation
- HPCA and ImmGen references
- for mouse, HPCA can be converted to mouse genes via the "biomart" method or by "lowercasing" it.
- Louvain, Louvain2, Leiden or SLM clustering algorithms
- multiple cluster resolutions
- in development : covariate analysis
It is recommended to run with the render script, which will create output files with timestamp of start time of the run
nohup Rscript QB_SingleCell_quickpass_render.R