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abc-enhancer-gene-prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

automator

bash4bioinformatics

Quick references to useful bash commands for bioinformatics

dreamlet-dev

Perform differential expression analysis on multi-sample single cell datasets using linear mixed models

esprnn

ESPRNN: Epigenome-based Splicing Prediction using Recurrent Neural Network

hoondy.github.io

Hoondy.com

hoondy.me

keras

Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano and TensorFlow.

mergebigwig

merge two or more bigWig files into one file by average

motiftools

TF Motif Variant Analysis

pegasus

pegasusio

pegasus io module for reading/writing single-cell genomics data

pyencoded-tools

rbm-ae-tf

Tensorflow 1.X implementation of Restricted Boltzman Machine(RBM) and Autoencoder with layerwise pretraining.

rna-seq-pipeline

scmyeloidad

Plasticity of Human Microglia and Brain Perivascular Macrophages in Aging and Alzheimer’s Disease

seurat

R toolkit for single cell genomics

signac

R toolkit for the analysis of single-cell chromatin data

starrpeaker

STARRPeaker: the STARR-seq peak caller

swalign

Smith-Waterman Algorithm in Perl

tflearn

Deep learning library featuring a higher-level API for TensorFlow.

zenith

Gene set analysis following differential expression using linear (mixed) modeling with dream