A pipeline for integrative analysis for scTCR- and scRNA-seq data
Project description
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
- Other python depedencies should be installed via
-
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
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
Project details
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