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
  ☆154Updated last year
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆166Updated 2 years ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆146Updated 4 months ago
• GoekeLab / m6anet
  Detection of m6A from direct RNA-Seq data
  ☆129Updated 7 months ago
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆174Updated last year
• epi2me-labs / wf-transcriptomes
  ☆109Updated last month
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆107Updated 2 years ago
• ay-lab / fithic
  Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…
  ☆92Updated 3 years ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆208Updated 3 months ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆123Updated last month
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆113Updated 4 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆92Updated 5 months ago
• epi2me-labs / pychopper
  cDNA read preprocessing
  ☆81Updated last year
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆117Updated 2 months ago
• Xinglab / rmats2sashimiplot
  ☆156Updated 7 months ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆105Updated 6 months ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆197Updated last week
• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆63Updated 3 years ago
• BioinfoUNIBA / REDItools
  REDItools are python scripts to investigate RNA editing at genomic scale.
  ☆69Updated 5 months ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆120Updated 3 weeks ago
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆166Updated last month
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆83Updated 3 years ago
• GoekeLab / xpore
  Identification of differential RNA modifications from nanopore direct RNA sequencing
  ☆159Updated last year
• mortazavilab / TranscriptClean
  Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
  ☆70Updated last year
• comprna / METEORE
  Automatic DNA methylation detection from nanopore tools and their consensus model
  ☆79Updated 2 years ago
• novoalab / EpiNano
  Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
  ☆117Updated 5 months ago
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆31Updated last month
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆61Updated 2 years ago
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆157Updated 4 months ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆174Updated last year