immunopipe 0.0.4

A pipeline for integrative analysis for scTCR- and scRNA-seq data

immunopipe

Integrative analysis for scTCR- and scRNA-seq data

Requirements & Installation

• python: 3.7+

  • Other python depedencies should be installed via pip install -U immunopipe

• R

  • immunarch(v0.6.7+), Seurat(v4.0+), scImpute, scran, scater
  • dplyr, tidyr, tibble, ggplot2, ggradar, ggprism, ggrepel, reshape2
  • ComplexHeatmap, RColorBrewer
  • future, parallel, gtools
  • enrichR

• Other

  • VDJtools: https://vdjtools-doc.readthedocs.io/en/master/install.html

Modules

• Basic TCR data analysis using immunarch
• Clone Residency analysis if you have paired samples (i.e. Tumor vs Normal)
• V-J usage, the frequency of various V-J junctions in circos-style plots
• Clustering cells and configurale arguments to separate T and non-T cells
• Clustering T cell, markers for each cluster and enrichment analysis for the markers
• Radar plots to show the composition of cells for clusters
• Markers finder for selected groups of cells
• Expression investigation of genes of interest for selected groups of cells
• UMAPs
• Metabolic landscape analysis (Ref: Xiao, Zhengtao, Ziwei Dai, and Jason W. Locasale. "Metabolic landscape of the tumor microenvironment at single cell resolution." Nature communications 10.1 (2019): 1-12.)

Documentaion

https://pwwang.github.io/immunopipe