Alternatives and similar repositories for chipseq:

Users that are interested in chipseq are comparing it to the libraries listed below

• snakemake-workflows / rna-seq-kallisto-sleuth
  A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
  ☆66Updated this week
• snystrom / memes
  An R interface to the MEME Suite
  ☆49Updated 4 months ago
• jokergoo / rGREAT
  GREAT Analysis - Functional Enrichment on Genomic Regions
  ☆86Updated 6 months ago
• kundajelab / phantompeakqualtools
  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…
  ☆56Updated 4 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆56Updated 4 years ago
• vivekbhr / Subread_to_DEXSeq
  Scripts to import your FeatureCounts output into DEXSeq
  ☆32Updated 6 years ago
• simonvh / bioinfosummer
  Tutorial for AMSI BioInfoSummer 2018
  ☆29Updated 6 years ago
• ucdavis-bioinformatics-training / 2017_2018-single-cell-RNA-sequencing-Workshop-UCD_UCB_UCSF
  2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF
  ☆35Updated 6 years ago
• NBISweden / workshop-epigenomics-RTDs
  workshop website on readthedocs
  ☆19Updated 2 months ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆54Updated this week
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆32Updated 2 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆80Updated 3 weeks ago
• sandberg-lab / Smart-seq3
  Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
  ☆51Updated 3 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆67Updated last month
• GoekeLab / proActiv
  Estimation of Promoter Activity from RNA-Seq data
  ☆50Updated 3 years ago
• jianhong / trackViewer
  A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot
  ☆69Updated last month
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆38Updated 3 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 3 months ago
• hamidghaedi / Enrichment-Analysis
  From RNA-seq raw reads to enriched pathways by DEGs
  ☆32Updated 9 months ago
• eQTL-Catalogue / qtlmap
  Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue
  ☆46Updated last week
• PhanstielLab / bedtoolsr
  R package wrapping bedtools
  ☆38Updated 5 months ago
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆66Updated 5 years ago
• maxsonBraunLab / gopeaks
  Peak caller for CUT&TAG data
  ☆25Updated 2 years ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• williamritchie / IRFinder
  Detecting intron retention from RNA-Seq experiments
  ☆54Updated 7 months ago
• ivanek / Gviz
  This is the Gviz development repository. Gviz plots data and annotation information along genomic coordinates.
  ☆79Updated 3 weeks ago
• menghaowei / ngstools
  My own tools code for NGS data analysis (Next Generation Sequencing)
  ☆29Updated 5 years ago
• dozmorovlab / excluderanges
  Genomic coordinates of problematic genomic regions as GRanges
  ☆35Updated 2 months ago
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 5 years ago
• morrislab / qapa
  RNA-seq Quantification of Alternative Polyadenylation
  ☆46Updated last year