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mgatk

mgatk: mitochondrial genome analysis toolkit

milopy

Python implementation of Milo for differential abundance testing on KNN graph

milor

R package implementation of Milo for testing for differential abundance in KNN graphs

motifboost

A library for the Immune Repertoire Classification Problem

netnmf-sc

netNMF-sc: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data

nextneopi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

novosparc

nxviz

Visualization Package for NetworkX

packcircles

A pure Python implementation of a circle packing algorithm

palantir

Single cell trajectory detection

patchwork

The Composer of ggplots

polyleven

Hyper fast Levenshtein distance library for Python

pybliometrics

Python-based API-Wrapper to access Scopus

pycirclize

Circular visualization in Python (Circos Plot, Chord Diagram)

pydantic

Data parsing and validation using Python type hints

pydeseq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

pyslingshot

Python implementation of the Slingshot pseudotime algorithm

quasr

receptor_utils

Misc utilities for receptor gene sequences

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scfea

single cell Flux Estimation Analysis (scFEA) Try the below web server!

scfunctions

Functions for single cell data analysis

schlacount

Count HLA alleles in single-cell RNA-seq data

scirpy

A scanpy extension to analyse single-cell TCR and BCR data.

scissor

Scissor package

single-cell-best-practices

https://www.sc-best-practices.org

tcrai

tcrdist3

flexible CDR based distance metrics

testrbuild

just a simple repo to hold workflows to check if R can be installed properly

troubleshooting_palantir

just to hold some notebooks as i troubleshoot palantir