Open Source Libs
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Open Source Libraries
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Chip Seq
37 Open Source Chip Seq Software Projects
Free and open source chip seq code projects including engines, APIs, generators, and tools.
Chip Seq Analysis
550 ⭐
ChIP-seq analysis notes from Ming Tang
Macs
530 ⭐
MACS -- Model-based Analysis of ChIP-Seq
Deeptools
494 ⭐
Tools to process and analyze deep sequencing data.
Snakepipes
271 ⭐
Customizable workflows based on snakemake and python for the analysis of NGS data
Galaxyproject Training Material
217 ⭐
A collection of Galaxy-related training material
Chipseq_pipeline
101 ⭐
AQUAS TF and histone ChIP-seq pipeline
Pyflow Chipseq
87 ⭐
a snakemake pipeline to process ChIP-seq files from GEO or in-house
Chipseq
96 ⭐
ChIP-seq peak-calling, QC and differential analysis pipeline.
Dolphinnext
81 ⭐
A graphical user interface for distributed data processing of high throughput genomics
Reg Gen
63 ⭐
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Haystack_bio
36 ⭐
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
Seq2science
81 ⭐
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.
Biocore Ntnu Epic
31 ⭐
(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
Gonetics
31 ⭐
Go / Golang Bioinformatics Library
Biotoolbox
24 ⭐
Tools for querying and analysis of genomic data
Deepstats
26 ⭐
deepStats: a stastitical toolbox for deeptools and genomic signals
Cruk Summer School 2018
22 ⭐
Summer school course materials collection
Bohdan Khomtchouk Microscope
20 ⭐
ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps
Pygtftk
26 ⭐
A python package and a set of shell commands to handle GTF files
Ggr Cwl
19 ⭐
CWL tools and workflows for GGR
Manorm
18 ⭐
A robust model for quantitative comparison of ChIP-Seq data sets.
Pybedgraph
17 ⭐
A Python package for fast operations on 1-dimensional genomic signal tracks
Marge
16 ⭐
API for HOMER in R for Genomic Analysis using Tidy Conventions
Cd4 Csaw
16 ⭐
Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
Alps
13 ⭐
AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project
Sevenc
11 ⭐
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Open_pipelines
14 ⭐
Pipelines for NGS data preprocessing by the Bock lab and friends
Afrendeiro Toolkit
12 ⭐
A toolkit for NGS analysis with Python
Chip Nf
12 ⭐
An automated ChIP-seq pipeline using Nextfow
Bioinf Commons
19 ⭐
Bioinformatics library in Kotlin
Harbourlab Spark
78 ⭐
Publication quality NGS track plotting
Ccbr Pipeliner
36 ⭐
An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
Manorm2
14 ⭐
MAnorm2 for Normalizing and Comparing ChIP-seq Samples
Ancetran
10 ⭐
AnceTran2.0: R package for transcriptome evolution analysis based on RNA-seq expression data or ChIP-seq TF-binding data
Tfregulomer
12 ⭐
TFregulomeR reveals transcription factors’ context-specific features and functions
Mspc
11 ⭐
Using combined evidence from replicates to evaluate ChIP-seq peaks
Protocols 4pub
28 ⭐
Multi-omics analysis protocols by Lyu.