yyoshiaki

langchain

🦜🔗 Build context-aware reasoning applications

nichenetr

NicheNet: predict active ligand-target links between interacting cells

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

bonito

A PyTorch Basecaller for Oxford Nanopore Reads

lab-website-template

An easy-to-use, flexible website template for labs.

cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

pytorch_mpiigaze_demo

Gaze estimation using MPIIGaze and MPIIFaceGaze

cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

scDRS

Single-cell disease relevance score (scDRS)

MultiVelo

Multi-omic velocity inference

MELD

Quantifying experimental perturbations at single cell resolution

milopy

Python implementation of Milo for differential abundance testing on KNN graph

scHLAcount

Count HLA alleles in single-cell RNA-seq data

cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

stitchr

Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info

tcr-bert

Large language modeling applied to T-cell receptor (TCR) sequences.

napari-spatialdata

Interactive visualization of spatial omics data

symphonypy

Port of symphony algorithm of single-cell reference atlas mapping to Python

allelefrequencies

📂 HLA allele frequencies in tab-delimited format, downloaded from AFND.

TiRP

code repository for Lagattuta et al. "Repertoire analyses reveal T cell receptor sequence features that influence T cell fate." Nat. Imm. (2022)

AnatPaste

Anatomy-aware self-supervised learning

gene2probe

Pipeline for designing custom probes against human genes

ImmCellTyper

Cytof data analysis toolkit

genal

Python module for genetic analyses

scDRS_paper

ReapTEC

ReapTEC pipeline to simultaneously profile gene expression and enhancer activity in 5' scRNA-seq datasets

ablang-util

util tools for ablang

cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

nf-core-reaptec