scRoadmap of multilineage cardiac differentiations manuscript

Source code for JBrowse 2, a modern React-based genome browser

code files related to the manuscript: Cell identity control coordinated by common and distinct transcription factors and associated gene regulatory networks in epidermal and corneal epithelia

MyGene.info: A BioThings API for gene annotations

Performant Pythonic GenomicRanges

Single Cell Epigenome-based Inference of Activity

Central repository for PhyloPic

Single cell ANANSE Gene-regulatory-network analysis from Seurat objects

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

SHOOT.bio - the phylogenetic search engine

Attraction-Repulsion Spectrum in Neighbor Embeddings

Fast-ish (and correct!) quantile normalization in Python.

From fastq to preprocessed Seurat object, compatable with Kallisto | Bustools (for instance, from the Seq2Science) workflow.

genes and genomes at your fingertips

The D4 Quantitative Data Format

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

Mypy stubs, i.e., type information, for numpy, pandas and matplotlib

The Fast Cross-Platform Package Manager

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples.