jianhong

trackViewer

A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot

ATACseqQC

ATAC-seq Quality Control

motifStack

Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

ChIPpeakAnno

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline. Hyperlink is an example of output index page.

ribosomeProfilingQC

An R package for quality assessment of ribosome profiling

scRNAseqApp

single cell RNA-seq results report system

GeneNetworkBuilder

Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data

genomictools

docker file for genomic tools

hicar

This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

NADfinder

Call wide peaks for sequencing data

threejsEpi

R version of Threejs

ATACseqTFEA

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

cdQuPath

Codex downstream analysis with QuPath

cleanUpdTSeq

This package classifies putative polyadenylation sites as true or false/internally oligodT primed

codex_qupath

The script collection for qupath

dagLogo

Visualize significant conserved amino acid sequence pattern in groups based on probability theory

enhancerHomologSearch

Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog region for given sequences

GenomicInteractionNodes

hicar_doc

hicVennDiagram

InPAS

Identification of Novel alternative PolyAdenylation Sites (PAS)

loopBouquetPlotDocumentation

The Documentation for loopBouquetPlot

merip

modules

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

pairedtag

A snakemake workflow for single-cell multiomic data analysis pipeline

prj_DD04XQ

collection of code for project DD04X

ratte

The use of RnA-seq for AnnoTation of Transpose Elements

scRNA-seq_notes

A list of scRNA-seq analysis tools