Stars
Ultimate Plumber is a tool for writing Linux pipes with instant live preview
Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.
A collaboratively written review paper on deep learning, genomics, and precision medicine
Predicting regulatory DNA elements based on epigenomic signatures
Deep learning for identifying cis-regulatory elements and other applications
dna2vec: Consistent vector representations of variable-length k-mers
Prediction of Active Enhancers and Promoters in a Cell type specific manner using shape matching of histone and/or DNase-I hypersensitivity profiles
HMMER: biological sequence analysis using profile HMMs
Analysis and Visualization of Ribosome Profiling Data
Visualization and analysis software for Hi-C data -
Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
UCSC Genome Browser source tree. Stable branch: "beta".
Git pre-commit hook that checks for Python PEP8 style compliance.
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
Python transpiler for the esoteric language Rockstar
Detecting Regulatory Elements using GRO-seq and PRO-seq
Tutorials covering various topics in genomic data analysis.
PARE: a computational method to Predict Active Regulatory Elements
Home of the Rockstar programming language