Alternatives and similar repositories for HiCExplorer

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

• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆227Updated this week
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆205Updated 3 weeks ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆202Updated this week
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 5 years ago
• vaquerizaslab / fanc
  FAN-C: Framework for the ANalysis of C-like data
  ☆115Updated last year
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆252Updated 4 months ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆409Updated last year
• akdemirlab / HiCPlotter
  “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
  ☆187Updated 4 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆215Updated 2 months ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆192Updated 2 years ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆275Updated last year
• ENCODE-DCC / rna-seq-pipeline
  ☆151Updated 2 years ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆229Updated this week
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆167Updated this week
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆269Updated last year
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆215Updated 5 months ago
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆95Updated 6 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆168Updated last week
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆212Updated 2 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆313Updated 4 years ago
• nf-core / hic
  Analysis of Chromosome Conformation Capture data (Hi-C)
  ☆99Updated 3 weeks ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆110Updated 2 years ago
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆211Updated this week
• open2c / cooltools
  The tools for your .cool's
  ☆152Updated 8 months ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆265Updated 2 years ago
• harvardinformatics / ATAC-seq
  ☆138Updated 6 years ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆181Updated 3 months ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆148Updated 9 months ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆229Updated last month