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align2rawsignal

A.K.A. WIGGLER: Creates genome-wide raw or normalized signal tracks from aligned sequencing reads (BAM/tagAlign)

annotables

R data package for annotating/converting Gene IDs

atacprimertool

Primer design for ATAC-qPCR

aupairwise

bam2tcc

bifet

A robust statistical test for TF footprint data analyses

biogridr

biogridr: BioGRID R API

bwtool

A tool for bigWig files.

chipseqspikeinfree

A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications

chromhmm

chromvar

chromatin Variability Across Regions (of the genome!)

circrna_finder

Pipeline for finding circular RNAs from RNA-seq data, based on STAR. Used in (Westholm et al, Cell Reports, 2014).

complexheatmap

make complex heatmaps as well as self define annotation graphics

conshmm

csvkit

A suite of utilities for converting to and working with CSV, the king of tabular file formats.

enhancedvolcano

Publication-ready volcano plots with enhanced colouring and labeling

enrichedheatmap

make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.

extract-transcript-regions

For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and CDS).

fishermp

FisherMP: Motif Prediction using Fisher's exact test with openMP Parallel design

gat

Genomic Association Tester

genie

A quick way into a systemd "bottle" for WSL

gg3d

A ggplot2 extension enabling 3D projections

ggpubr

'ggplot2' Based Publication Ready Plots

haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

homer-idr

Applying IDR analysis to Homer peaks.

homerkit

Read HOMER motif analysis output in R.

makegencodetss

Makes distinct TSS of each gene from a Gencode annotation

networkd3

D3 JavaScript Network Graphs from R

ngstools

Next-Generation Sequencing(NGS) toolkits.

nlputilitybelt

Auxiliary NLP tools