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+
dplyr
tidyr
tibble
ggplot2
ggradar
ggprism
ggrepel
future
parallel
enrichR
ComplexHeatmap
-
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
Documentaion
Project details
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