Helpers for working with ChromHMM (http://compbio.mit.edu/ChromHMM/)
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Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing
Miscellaneous tools for genomics
BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
Demos a Snakemake workflow to classify enhancer regions based on publicly available chromatin marks.
HiM library design tools
Quickly get the taxonomy of a genome
Python bindings to UCSC BigWig and BigBed library
Targeted Detection and Reconstruction of Plasmids
This repository hosts a minimal version of a Python API for BPNet.
Python utilities for building integrated views of TCGA data.
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data
Alignment and antibody assembly pipelines for Croote et al. (Science, 2018)
Convert UCSC's ENCODE metadata into pandas DataFrames