Stars
An opinionated list of awesome Python frameworks, libraries, software and resources.
Single-cell analysis in Python. Scales to >100M cells.
Unifying Variational Autoencoder (VAE) implementations in Pytorch (NeurIPS 2022)
Collection of bioinformatics training materials
RNAseq analysis notes from Ming Tang
Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
A tool to find sequencing data and metadata from public databases.
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene reg…
Tools for handling Unique Molecular Identifiers in NGS data sets
A template repo for Python packages
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
A scanpy extension to analyse single-cell TCR and BCR data.
🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
Differential expression analysis for single-cell RNA-seq data.
A scalable SCENIC workflow for single-cell gene regulatory network analysis
A collection of best practice cookiecutter templates for all domains and languages with extensive Github support ⛺
Episcanpy: Epigenomics Single Cell Analysis in Python
Fast and accurate in silico inference of HLA genotypes from RNA-seq
Subpopulation detection in high-dimensional single-cell data
A template for standard compliant snakemake-workflows
Python interface to running command-line and web-based MHC binding predictors
dpeerlab / PhenoGraph
Forked from jacoblevine/PhenoGraphSubpopulation detection in high-dimensional single-cell data
Compute generation probabilities of CDR3 amino acid and nucleotide sequences