Alternatives and similar repositories for hic

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

• mortazavilab / TALON
  Technology agnostic long read analysis pipeline for transcriptomes
  ☆149Updated last year
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆135Updated 3 weeks ago
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆172Updated last year
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆158Updated 2 years ago
• epi2me-labs / wf-transcriptomes
  ☆103Updated last month
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆90Updated last month
• ay-lab / fithic
  Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…
  ☆89Updated 3 years ago
• mortazavilab / TranscriptClean
  Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
  ☆69Updated last year
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆117Updated 7 months ago
• epi2me-labs / pychopper
  cDNA read preprocessing
  ☆78Updated last year
• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆62Updated 3 years ago
• GoekeLab / m6anet
  Detection of m6A from direct RNA-Seq data
  ☆129Updated 3 months ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆151Updated last month
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆116Updated 3 weeks ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• BioinfoUNIBA / REDItools2
  ☆58Updated last month
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆203Updated 2 weeks ago
• cortes-ciriano-lab / savana
  Somatic structural variant caller for long-read data
  ☆80Updated 3 months ago
• Oshlack / JAFFA
  JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
  ☆98Updated 3 months ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆114Updated 3 years ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆179Updated last week
• BioinfoUNIBA / REDItools
  REDItools are python scripts to investigate RNA editing at genomic scale.
  ☆68Updated last month
• gencorefacility / variant-calling-pipeline-gatk4
  Variant Calling Pipeline Using GATK4 and Nextflow
  ☆58Updated 2 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆170Updated last year
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆92Updated 3 months ago
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆111Updated 4 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆149Updated this week
• biocorecrg / master_of_pores
  Nextflow pipeline for analysis of direct RNA Nanopore reads
  ☆106Updated 2 months ago