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
- A bunch of R packages
-
Other
-
Checking requirements
pip install -U pipen-cli-require pipen require immunopipe.pipeline:pipeline <pipeline arguments>
-
Quick way to install the dependencies using conda
conda env install --name <env_name> --file docker/environment.yml # then conda activate <env_name>
Running as a container
Using docker:
docker run \
-w /immunopipe/workdir \
-v $(pwd)/:/immunopipe/workdir \
-v /tmp \
-v $(pwd)/prepared-data:/mnt \
justold/immunopipe:<tag> # or :dev to use the development version
Using singularity:
singularity run -w \ # need it to be writable
--pwd /immunopipe/workdir -B .:/immunopipe/workdir \ # Could use other directory instead of "."
# --contain: don't map host filesystem
# --cleanenv: recommended, to avoid other host's environment variables to be used
# For example, $CONDA_PREFIX to affect host's conda environment
--contain --cleanenv \
docker://justold/immunopipe:<tag> # or :dev to use the development version
# The mount your data directory to /mnt, which will make startup faster
# For example
# -B .:/immunopipe/workdir,/path/to/data:/mnt
# Where /path/to/data is the data directory containing the data files
# You may also want to bind other directories (i.e. /tmp)
# -B <other bindings>,/tmp
# Or you can pull the image first by:
singularity pull --force --dir images/ docker://justold/immunopipe:<tag>
# Then you can replace "docker://justold/immunopipe:<tag>" with "images/immunopipe.sif"
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
- (Meta-)Markers finder for selected groups/clones of cells
- Psedo-bulk GSEA analysis of two groups of cells
- Seurat cluster statistics, including:
- Basic statistics of the clusters (e.g. number of cells in each cluster)
- Gene expressions (e.g. ridge, violin, feature, dot and heatmap plots)
- Dimensional reduction plots
- TCR clustering using CDR3 sequences and the statistics of the clusters
- Cell group distribution (TCR clones/clusters) in Seurat clusters
- Clone heterogeneity (TCR clone distribution) in Seurat clusters
- 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
Example
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
immunopipe-0.5.1.tar.gz
(25.4 kB
view hashes)
Built Distribution
immunopipe-0.5.1-py3-none-any.whl
(28.4 kB
view hashes)
Close
Hashes for immunopipe-0.5.1-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 34ffa36df298242b622b1fefb0689e945bcf01649b1e2f8d42af0468d8c801bd |
|
MD5 | 8cd13896f0def14cac5205324b6ea775 |
|
BLAKE2b-256 | 2ae3b95653f5582c3b4a10c5589da15db60c45e9ca5f0b8b10094f89636db96e |