Alternatives and similar repositories for chromap:

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

• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆215Updated last week
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆210Updated this week
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆273Updated 9 months ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆109Updated 2 years ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆246Updated 2 months ago
• nf-core / hic
  Analysis of Chromosome Conformation Capture data (Hi-C)
  ☆99Updated 2 months ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆244Updated 4 months ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆161Updated this week
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆170Updated 9 months ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆127Updated 2 months ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆121Updated 2 years ago
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆140Updated last year
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆112Updated 2 years ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆179Updated 3 weeks ago
• saketkc / gencode_regions
  Extract 3'UTR, 5'UTR, CDS, Promoter, Genes, Introns, Exons from GTF files
  ☆107Updated 3 years ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆147Updated 2 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆215Updated 9 months ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆189Updated last year
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆200Updated last month
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆244Updated last month
• harvardinformatics / ATAC-seq
  ☆131Updated 6 years ago
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆206Updated this week
• mortazavilab / TALON
  Technology agnostic long read analysis pipeline for transcriptomes
  ☆142Updated last year
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆112Updated 8 months ago
• epi2me-labs / wf-transcriptomes
  ☆90Updated 3 months ago
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆158Updated 5 months ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆159Updated 7 months ago
• epi2me-labs / wf-single-cell
  ☆86Updated 3 weeks ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆220Updated 2 weeks ago