From: scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing
Command | Description | Input | Output |
---|---|---|---|
scAnalyzer | Main program to perform full scRNA-seq data analysis with QC and data harmonization | A path to analysis config file (config.yml) | Final analysis results in h5ad and h5Seurat format |
scDEG | Program to perform DEG analysis between two phenotypes within each cluster of an annotation (such as cell types) | A path to a DEG config file (config_DEG.yml) | One DEG table for each cluster and an SQLite db file of all comparisons |
scRef | Program to create Seurat 'Azimuth' references | A path to a reference config file (config_ref.yml) | An RDS object with 'Azimuth' reference for scAnalyzer |
sc2celldepot | Program to transfer analyzed data into h5ad for the cellxgene VIP (CellDepot) loading | A path to a data config file (config_convert.yml) | An h5ad file |
scTool | Tool to add, remove or export express/annotation from an h5ad file | A path to an h5ad file | A modified h5ad file or a csv file |
scRMambient | Program to remove ambient RNA by CellBender | A path to a sample metadata file containing paths to raw (unfiltered) UMI along with a few CellBender parameters | CellBender filtered UMI counts in h5 format |