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

Annotated data.

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…

Joyplots in Python with matplotlib & pandas 📈

Geometry-preserving random sampling

Episcanpy: Epigenomics Single Cell Analysis in Python

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

Convert between AnnData and SingleCellExperiment

Mapping out the coarse-grained connectivity structures of complex manifolds.

RNA velocity estimation in Python

Single-cell analysis in Python. Scales to >1M cells.

python module to plot beautiful and highly customizable genome browser tracks

A python extension for quick access to bigWig and bigBed files

Log command line events to a graph database :)

Official git repository for Biopython (originally converted from CVS)

de novo sequence assembler using string graphs

Patch for GNU make v 4.0 including new functions

Rna-seq pipeline, From FASTQ to differential expression analysis...

q - Run SQL directly on delimited files and multi-file sqlite databases

Provides easy read/write access to genomic tracks

EpiExplorer is a web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborous preprocessing.

Tools to process and analyze deep sequencing data.