Alternatives and similar repositories for liftover

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

• liguowang / CrossMap
  CrossMap is a python program to lift over genome coordinates from one genome version to another.
  ☆86Updated 2 months ago
• freeseek / score
  Tools to work with GWAS-VCF summary statistics files
  ☆122Updated last month
• igvteam / igv-notebook
  Module for embedding igv.js in an IPython notebook
  ☆78Updated 7 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
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆116Updated last month
• ygidtu / trackplot
  trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and fu…
  ☆97Updated last week
• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆120Updated last year
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆74Updated last year
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆114Updated 3 years ago
• kircherlab / CADD-scripts
  CADD scripts release for offline scoring. For more information about CADD, please visit our website
  ☆85Updated 3 months ago
• phageghost / python-genome-browser
  Tools for making plots of genomic datasets in a genome-browser-like format
  ☆32Updated 9 months ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆75Updated last year
• konstantint / pyliftover
  Pure-python implementation of UCSC liftOver genome coordinate conversion
  ☆97Updated last year
• 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
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆71Updated last year
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆80Updated 10 months ago
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆89Updated 2 months ago
• ENCODE-DCC / hic-pipeline
  HiC uniform processing pipeline
  ☆61Updated last year
• gatk-workflows / gatk4-rnaseq-germline-snps-indels
  Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
  ☆80Updated 4 years ago
• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆63Updated 3 years ago
• odelaneau / shapeit5
  Segmented HAPlotype Estimation and Imputation Tool
  ☆86Updated 3 weeks ago
• Genotek / ClassifyCNV
  ClassifyCNV: a tool for clinical annotation of copy-number variants
  ☆66Updated 2 years ago
• broadinstitute / pyqtl
  Collection of analysis tools for quantitative trait loci
  ☆58Updated this week
• ShujiaHuang / qmplot
  A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.
  ☆47Updated last year
• vanallenlab / comut
  CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
  ☆95Updated last year
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 7 months ago
• nloyfer / meth_atlas
  ☆50Updated 3 years ago