Alternatives and similar repositories for genome-tools

Users that are interested in genome-tools are comparing it to the libraries listed below

• paulsengroup / hictk
  Blazing fast toolkit to work with .hic and .cool files
  ☆41Updated this week
• rjdkmr / gcMapExplorer
  Genome Contact Map Explorer - gcMapExplorer. Visit:
  ☆21Updated 3 years ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆63Updated 6 months ago
• seqcode / allo
  Allo: a multi-mapped read rescue strategy for gene regulatory analyses
  ☆24Updated last year
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated last year
• maxplanck-ie / HiCAssembler
  Software to assemble contigs/scaffolds into chromosomes using Hi-C data
  ☆28Updated last year
• deeptools / HiCMatrix
  ☆13Updated 2 months ago
• ulelab / ultraplex
  Ultra-fast 5' and 3' demultiplexer
  ☆28Updated last year
• Xinglab / isoCirc
  isoCirc
  ☆10Updated last year
• complextissue / pytximport
  Feature-rich Python implementation of the tximport package for gene count estimation.
  ☆37Updated 3 weeks ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated last year
• pinellolab / AmpUMI
  Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
  ☆41Updated 2 months ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆39Updated last year
• timplab / nanoNOMe
  nanoNOMe (Nucleosome Occupancy and Methylome nanopore sequencing) Analysis
  ☆20Updated 2 years ago
• brentp / cigar
  simple library for dealing with SAM cigar strings
  ☆41Updated 4 years ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆44Updated 3 years ago
• Oshlack / Clinker
  Gene Fusion Visualiser
  ☆51Updated 2 years ago
• nspies / svviz2
  for visual evaluation of read support for structural variation
  ☆55Updated last year
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• ncbi / BAMscale
  BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy …
  ☆72Updated 11 months ago
• agalitsyna / RedClib
  Red-C data processing
  ☆15Updated 2 years ago
• LosicLab / starchip
  Detection of Circular RNA and Fusions from RNA-Seq
  ☆32Updated 7 years ago
• mortazavilab / lapa
  Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
  ☆31Updated 2 years ago
• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆69Updated 2 months ago
• cmdoret / hicreppy
  Python reimplementation of hicrep with compatibility for sparse matrices
  ☆18Updated 2 years ago
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆27Updated 2 years ago
• refgenie / refgenie
  Reference genome resource manager
  ☆74Updated last year
• gagneurlab / absplice
  ☆39Updated 4 months ago
• LappalainenLab / lorals
  ☆38Updated 2 years ago
• hms-dbmi / chromoscope
  Interactive multiscale visualization for structural variation in human genomes
  ☆70Updated last week