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
  ☆151Updated last year
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆172Updated last year
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆138Updated last month
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆158Updated 2 years ago
• epi2me-labs / wf-transcriptomes
  ☆104Updated 2 months ago
• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆63Updated 3 years ago
• GoekeLab / m6anet
  Detection of m6A from direct RNA-Seq data
  ☆129Updated 4 months ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆204Updated 2 weeks ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆90Updated 2 months ago
• nf-core / differentialabundance
  Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
  ☆82Updated last week
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆150Updated last month
• BioinfoUNIBA / REDItools
  REDItools are python scripts to investigate RNA editing at genomic scale.
  ☆68Updated 2 months ago
• mortazavilab / TranscriptClean
  Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
  ☆69Updated last year
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆117Updated 8 months ago
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆29Updated 8 months ago
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆160Updated this week
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆104Updated 4 months ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆116Updated 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
• StevenWingett / FastQ-Screen
  Detecting contamination in NGS data and multi-species analysis
  ☆78Updated 11 months ago
• epi2me-labs / pychopper
  cDNA read preprocessing
  ☆78Updated last year
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆82Updated 3 years ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆239Updated last week
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆125Updated 3 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆171Updated last year
• broadinstitute / long-read-pipelines
  Long read production pipelines
  ☆148Updated this week
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆112Updated 4 years ago