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Uniform Manifold Approximation and Projection

Official git repository for Biopython (originally converted from CVS)

This is the development home of the workflow management system Snakemake. For general information, see

Single-cell analysis in Python. Scales to >100M cells.

Deep probabilistic analysis of single-cell and spatial omics data

🧬 gget enables efficient querying of genomic reference databases

Supplementary files for my book, "Bioinformatics Data Skills"

RedNotebook is a cross-platform journal

Spatial Single Cell Analysis in Python

CellRank: dynamics from multi-view single-cell data

Benchmarking analysis of data integration tools

Code, unit tests, and tutorials for running PICRUSt2

Download FASTQ files from SRA or ENA repositories.

Single cell perturbation prediction

Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)

Differential expression analysis for single-cell RNA-seq data.

web-based analysis tool for rare disease genomics

Clustering scRNAseq by genotypes

Bench-marking classification tools for scRNA-seq data

Python framework for Systems Biology modeling

Batch balanced KNN

Tools for single-cell data processing

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Statistical Analysis of Metagenomic Profiles

Demultiplexing pooled scRNA-seq data with or without genotype reference

Snakemake pipeline that works with the scIB package to benchmark data integration methods.

A flexible and extensible API for annotated 2D matrix data stored in multiple underlying formats.

Accelerated, Python-only, single-cell integration benchmarking metrics

Bioinformatics on GCP, AWS or Azure