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pylearn2

A Machine Learning library based on Theano

python_reading_group

query_speed_test

testing querying various backends (i.e. tiledb, hdf5, bigwig)

retina-models

BPNet models for retina single-cell multiome data

revcomp_experiments

rnapred

Code for RNA-seq prediction based on chromatin and exon arrays

sambamba

Tools for working with SAM/BAM/CRAM data

sambamba-docker

dockerfile for our sambamba fork

samstats

Georgi's scripts to compute mapping statistics. An alternative to flagstat

seqdataloader

Sequence data label generation and ingestion into deep learning models

seqmotif

Sequence motif visualization

seqpriorizationcatlas

Sequence priorization using gkm-explain.

shap

A unified approach to explain the output of any machine learning model.

shogunscripts

These scripts were written by Irene Kaplow for running Shogun with various kernels.

simdna

A python library for creating simulated regulatory DNA sequences

simdna_dragonn

simdna version for dragonn

snapatac

Analysis Pipeline for Single Cell ATAC-seq

svm_pipelines

tf-atlas

Code repository for the TF-Atlas project

tf-singularity

Tensorflow singularity container

tf_binding_challenge

scoring/ranking code for tf binding challenge

tfmodisco

TF MOtif Discovery from Importance SCOres

tfmodisco_bio_experiments

theano

Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It can use GPUs and perform efficient symbolic differentiation.

training_camp

Genetics training camp

tronn

Transcriptional Regulation (Optimized) Neural Nets (TRoNN)

undead

Need an obsolete Phobos module? Here they are, back from the dead and upgraded to work with the latest D

veryolddontuse_deeplift_modisco_tutorial

visualizer

Find and organize genome data files and visualize them with WashU Epigenome Browser

vizsequence

Collecting commonly-repeated sequence visualization code here