Alternatives and similar repositories for HiC-Pro

Users that are interested in HiC-Pro are comparing it to the libraries listed below

• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆249Updated 5 months ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆201Updated 3 weeks ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆308Updated 4 years ago
• Xinglab / rmats-turbo
  ☆260Updated 6 months ago
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆215Updated 3 weeks ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆280Updated 10 months ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆265Updated 2 years ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆306Updated 2 years ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆418Updated 10 months ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆295Updated 2 years ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆251Updated 3 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆266Updated last year
• ENCODE-DCC / chip-seq-pipeline2
  ENCODE ChIP-seq pipeline
  ☆267Updated last year
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated last week
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆215Updated 4 months ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆341Updated 10 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆224Updated this week
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆275Updated 11 months ago
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆442Updated 6 months ago
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆191Updated 2 weeks ago
• ENCODE-DCC / rna-seq-pipeline
  ☆151Updated 2 years ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆442Updated last year
• akdemirlab / HiCPlotter
  “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
  ☆187Updated 4 years ago
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆242Updated 2 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆211Updated last month
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆241Updated 2 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆167Updated last week
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆465Updated 2 weeks ago
• kundajelab / atac_dnase_pipelines
  ATAC-seq and DNase-seq processing pipeline
  ☆165Updated 2 years ago