Alternatives and similar repositories for Cut-and-Run

Users that are interested in Cut-and-Run are comparing it to the libraries listed below

• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 8 months ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆70Updated 6 months ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆58Updated last month
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆59Updated 4 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆81Updated 5 months ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆43Updated 7 years ago
• vivekbhr / Subread_to_DEXSeq
  Scripts to import your FeatureCounts output into DEXSeq
  ☆33Updated 6 years ago
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 3 years ago
• williamritchie / IRFinder
  Detecting intron retention from RNA-Seq experiments
  ☆55Updated 11 months ago
• parklab / ShatterSeek
  ☆69Updated 2 years ago
• francois-a / fastqtl
  Enhanced version of the FastQTL QTL mapper
  ☆67Updated 2 years ago
• crazyhottommy / pyflow-scATACseq
  snakemake workflow for post-processing scATACseq data
  ☆22Updated 5 years ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆115Updated 5 months ago
• zhqingit / giremi
  GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
  ☆44Updated 8 years ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆56Updated 4 years 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…
  ☆59Updated 4 years ago
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 6 years ago
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆65Updated 6 years ago
• smithlabcode / methpipe
  A pipeline for analyzing DNA methylation data from bisulfite sequencing.
  ☆70Updated 2 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• eQTL-Catalogue / qtlmap
  Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue
  ☆49Updated 3 weeks ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• jernst98 / ChromHMM
  ☆87Updated last week
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆35Updated 2 years ago
• nskvir / RepEnrich
  RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆27Updated 3 years ago
• khuang28jhu / bs3
  BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
  ☆27Updated 6 years ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• simonvh / bioinfosummer
  Tutorial for AMSI BioInfoSummer 2018
  ☆29Updated 6 years ago
• Xinglab / CLAM
  CLIP-seq Analysis of Multi-mapped reads
  ☆31Updated 3 years ago