scrna-recom

A collected resource for scRNA-seq data analysis with biomedical applications

Packages

We provide two packages wrapped with common used tools in scRNA-seq analysis.

• scrnaRecom (R)

  • quality control: DoubletFinder, Seurat
  • integration: Seurat CCA, Seurat RPCA, Liger and Harmony
  • reduction and clustering: Seurat
  • cell annotation: singleR，scCATCH, CellMarker
  • trajectory prediction: Monocle3
  • cell communication: CellChat
  • metabolic flux: scMetabolism

• pyscrnarecom (Python)

  • rawdata analysis: cellranger
  • quality control, reduction and cluster: scanpy
  • regulon analysis: pySCENIC
  • trajectory prediction: scVelo
  • metabolic analysis: scFEA

Installation

Details

Please add the library exec directory to PATH

Usage

scrnaRecom

Excutable commands are available under the scrnaRecom/exec folder after installation.

quality control

integration

reduction and clustering

cell annotation

pyscrnarecom

Excutable commands are available under the current environment after installation.

raw data analysis

basic analysis: qc, reduction, and clustering

trajectory inference

regulon analysis

metabolic analysis