Detecting Regulatory Elements using GRO-seq and PRO-seq

An algorithm to detect nascent RNA transcription in GRO-seq and ChIP-seq

Identifies Pol II 'waves' in GRO-seq or PRO-seq with support for bigWig files.

Tools to process and analyze deep sequencing data.

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

Extract 3D contacts (.pairs) from sequencing alignments

The tools for your .cool's

HemTools: a collection of NGS pipelines and bioinformatic analyses

A toolkit for analyzing architectural stripes

Analysis of gene expression and splicing diversity in a subset of samples from the 1000 Genomes Project, including eQTL and sQTL discovery and annotation.

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

Draw heatmap simply using a tidy data frame

Visualization of a correlation matrix using ggplot2

Extended tools for correlation analysis and visualization.

Tile-able heatmaps using ggheatmap and patchwork

ggplot2 version of heatmap

Make Complex Heatmaps

Pretty heatmaps

Display and analyze ROC curves in R and S

Scanning and visualization for variable gap motifs.

Genome-wide contact analysis using sklearn

Ultrafast GPU-enabled QTL mapper

Supplementary files and notebooks to recreate figures.

Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C and more. Runs on single machine, Hadoop, Spark, Dask, Flink and DataFlow

Converts fastq.gz files for a sample into bigwig tracks for data visusalization on UCSC browser or IGV.

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

Repository to host tool-specific module files for the Nextflow DSL2 community!

Analysis of Chromosome Conformation Capture data (Hi-C)