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ChIP-seq-analysis crazyhottommy

295

755

mit

65

ChIP-seq analysis notes from Ming Tang

chip-seq histone-modifications transcription-factor-binding

Created 2015-06-12

364 commits to master branch, last one 4 months ago

MACS macs3-project

269

717

bsd-3-clause

48

MACS -- Model-based Analysis of ChIP-Seq

macs python atac-seq chip-seq dnase-seq peak-caller poisson-equation

Created 2011-03-02

1,675 commits to master branch, last one 25 days ago

deepTools deeptools

212

691

other

43

Tools to process and analyze deep sequencing data.

ngs python rna-seq chip-seq genomics bioinformatics

Created 2013-07-08

3,487 commits to master branch, last one 9 months ago

snakepipes maxplanck-ie

87

389

unknown

20

Customizable workflows based on snakemake and python for the analysis of NGS data

ngs hi-c rna-seq atac-seq chip-seq workflow snakemake bisulfite-sequencing

Created 2016-03-23

4,059 commits to master branch, last one 2 months ago

training-material galaxyproject

923

312

mit

51

A collection of Galaxy-related training material

ngs rnaseq chip-seq training tutorial materials usegalaxy proteomics metagenomics hacktoberfest

Created 2015-06-29

29,187 commits to main branch, last one 2 days ago

ChIPseeker YuLab-SMU

76

231

unknown

20

:dart: ChIP peak Annotation, Comparison and Visualization

atac-seq chip-seq annotation comparison epigenetics epigenomics visualization

Created 2014-05-31

927 commits to devel branch, last one about a month ago

chipseq nf-core

150

200

mit

148

ChIP-seq peak-calling, QC and differential analysis pipeline.

chip macs2 nf-core chip-seq nextflow pipeline workflow peak-calling chromatin-immunoprecipitation

Created 2018-04-24

1,835 commits to master branch, last one 2 months ago

seq2science vanheeringen-lab

27

156

mit

6

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

ngs sra fastq rna-seq atac-seq chip-seq pipeline snakemake workflows bioinformatics reproducible-research bioinformatics-pipeline

Created 2019-07-11

1,483 commits to master branch, last one 10 months ago

SparK harbourlab

20

108

unknown

5

Publication quality NGS track plotting

igv ngs rna-seq chip-seq plotting ngs-analysis bedgraph-files

Created 2019-11-14

334 commits to master branch, last one 2 years ago

chipseq_pipeline kundajelab

40

106

bsd-3-clause

40

AQUAS TF and histone ChIP-seq pipeline

chip-seq genomics chip-seq-pipelines

Created 2015-07-16

811 commits to master branch, last one 5 years ago

reg-gen CostaLab

30

106

other

11

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

ngs motif atac-seq chip-seq genomics dnase-seq footprinting bioinformatics motif-analysis differential-peak-calling

Created 2015-06-17

2,898 commits to master branch, last one about a year ago

differentialabundance nf-core

40

66

mit

150

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

gsea limma shiny deseq2 nf-core rna-seq atac-seq chip-seq nextflow pipeline workflow microarray differential-abundance differential-expression

Created 2022-10-12

1,105 commits to master branch, last one 7 months ago

Protocols-4pub sajuukLyu

13

49

gpl-3.0

3

Multi-omics analysis protocols by Lyu.

wgbs rna-seq atac-seq chip-seq

Created 2021-03-08

49 commits to main branch, last one about a year ago

BioSeqUtils junjunlab

2

31

other

2

Extract Sequence from Genome According to Annotation File

gtf hic genome atac-seq chip-seq merip-seq transcript coverage-plot

Created 2023-03-03

80 commits to master branch, last one about a month ago