19 projects
tangermeme
Biological sequence analysis for the modern age.
bam2bw
A command-line tool for converting SAM/BAM files into stranded bp resolution BigWig files.
pomegranate
A PyTorch implementation of probabilistic models.
modisco-lite
Transcription Factor MOtif Discovery from Importance SCOres - lite
bpnet-lite
bpnet-lite is a minimal implementation of BPNet, a neural network aimed at interpreting regulatory activity of the genome.
modisco
TF MOtif Discovery from Importance SCOres
dragonnfruit
dragonnfruit is a method for analyzing scATAC-seq experiments.
ledidi
Ledidi is an optimization approach for designing edits to biological sequences.
torchegranate
A rewrite of pomegranate using PyTorch.
yuzu-ism
yuzu implements a compressed-sensing based approach for speeding up saliency calculations.
avocado-epigenome
Avocado is a package for learning a latent representation of the human epigenome.
apricot-select
apricot is a package for submodular selection of representative sets for machine learning models.
kiwano
Kiwano is an implementation of an approach for prioritizing epigenomic and transcriptomic experiments.
rambutan
rambutan is a python wrapper for caffe, aiming to provide a simpler way to define, train, and evaluate models.
pythonic-porin
Nanopore Data Analysis package. Provides tools for reading data, performing event detection, segmentation, visualization, and analysis using hidden Markov models, and other tools. Designed for the UCSC Nanopore Group.
yahmm
YAHMM is a HMM package for Python, implemented in Cython for speed.
antz
antz is a bioinformatics package written for python.
yabn
YABN is a Bayesian Network package for Python, implemented in Cython for speed.
discern
DISCERN is a method for identifying perturbations between two similar graphs. It takes in samples from two networks, and identifies which features are conditionally dependent on different features between the two
