Alternatives and similar repositories for HiCExplorer:

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

• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆394Updated 10 months ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆196Updated 2 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆240Updated last week
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆196Updated this week
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆206Updated this week
• vaquerizaslab / fanc
  FAN-C: Framework for the ANalysis of C-like data
  ☆109Updated 11 months ago
• open2c / cooltools
  The tools for your .cool's
  ☆144Updated 3 months ago
• akdemirlab / HiCPlotter
  “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
  ☆183Updated 4 years ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆190Updated last year
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆207Updated 3 weeks ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆122Updated 4 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆261Updated last year
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆142Updated 5 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆202Updated 3 months ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆107Updated 2 years ago
• ENCODE-DCC / rna-seq-pipeline
  ☆146Updated 2 years ago
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆197Updated this week
• hms-dbmi / hic-data-analysis-bootcamp
  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
  ☆194Updated 6 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆181Updated 3 weeks ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆268Updated 7 months ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆287Updated last year
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆288Updated 3 years ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆155Updated last week
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆119Updated 2 years ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆174Updated 2 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆204Updated this week
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆99Updated 3 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆157Updated last week
• nf-core / hic
  Analysis of Chromosome Conformation Capture data (Hi-C)
  ☆95Updated 2 weeks ago