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Table 1 Pipeline scripts and their function

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