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activityinequality

Data release for Activity Inequality paper

afterqc

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

allelecounter

Counts the number of reads which map to either the reference or alternate allele at each heterozygous SNP.

allelespecificatacseq

atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

backspin

Biclustering algorithm

bedtools-python

A Python interface to the BEDTools API using Cython

bfc

High-performance error correction for Illumina resequencing data

bgt

Flexible genotype query among 30,000+ samples whole-genome

biopieces

Biopieces is a bioinformatic framework of tools easily used and easily created.

bipolarcell2016

bootswatch

Themes for Bootstrap

brainmapr

R package to infer spatial location of neuronal subpopulations within the developing mouse brain by integrating single-cell RNA-seq data with in situ RNA patterns from the Allen Developing Mouse Brain Atlas

butlrtools

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

capstone

Capstone project

capstoneprojectsw

SW for the Coursera Capstone Project Data Science Specilization

caret

caret (Classification And Regression Training) R package that contains misc functions for training and plotting classification and regression models

cellnet

centipede.tutorial

:bug: How to use CENTIPEDE to determine if a transcription factor is bound.

chromvar

chromatin Variability Across Regions (of the genome!)

chromvarmotifs

R package with motifs for use with chromVAR

clustering_on_transcript_compatibility_counts

Clustering cells from single cell RNA seq assays

cooler

A cool place to store your Hi-C

course_project_devdataprod

course_project_samsung_data

courses

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1

cshl-singlecell-2017

Single Cell Analysis course at Cold Spring Harbor Laboratory 2017

cutadapt

cutadapt removes adapter sequences from sequencing reads