Alternatives and similar repositories for PARE

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

• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆37Updated 3 years ago
• lamortenera / epicseg
  Chromatin segmentation in R
  ☆19Updated 7 years ago
• Danko-Lab / rtfbs_db
  Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
  ☆22Updated 6 years ago
• rajanil / msCentipede
  A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
  ☆26Updated 8 years ago
• ratschlab / mmr
  A tool for Read Multi-Mapper Resolution
  ☆23Updated 8 years ago
• ParkerLab / atactk
  A toolkit for working with ATAC-seq data.
  ☆24Updated 11 months ago
• CollasLab / edd
  Enriched Domain Detector for ChIP-seq data
  ☆16Updated 2 years ago
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆30Updated 6 years ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆31Updated 2 years ago
• pachterlab / aggregationDE
  Scripts and software supplement for "Gene-level differential analysis at transcript-level resolution" by Yi, Pimentel, Bray and Pachter
  ☆19Updated 7 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• Jfortin1 / TCGA_AB_Compartments
  A/B compartments for 12 cancer types estimated from TCGA methylation data
  ☆20Updated 8 years ago
• Simon-Coetzee / motifBreakR
  A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
  ☆29Updated 10 months ago
• yuchaojiang / SCALE
  Allele-Specific Expression by Single-Cell RNA Sequencing
  ☆28Updated 4 years ago
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• hall-lab / gtex
  GTEx analysis scripts
  ☆20Updated 8 years ago
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 9 years ago
• churchill-lab / emase
  Expectation-Maximization algorithm for Allele-Specific Expression
  ☆21Updated 2 years ago
• markrobinsonuzh / diff_splice_paper
  Code for differential splicing comparison paper (Soneson, Matthes, et al.)
  ☆20Updated 8 years ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• mikelove / alpine
  Modeling and correcting fragment sequence bias for RNA-seq
  ☆24Updated last year
• brwnj / umitools
  Tools to handle reads sequenced with unique molecular identifiers (UMIs).
  ☆30Updated 7 years ago
• Danko-Lab / tutorials
  Tutorials covering various topics in genomic data analysis.
  ☆17Updated 6 years ago
• ChristopherWilks / snaptron
  fast webservices based query tool for large sets of genomic features
  ☆25Updated 3 weeks ago
• AstraZeneca-NGS / disambiguate
  Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem
  ☆31Updated 7 years ago
• databio / MIRA
  R package for Methylation-based Inference of Regulatory Activity
  ☆13Updated 5 years ago
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• jernst98 / ChromImpute
  ☆16Updated last year
• kauralasoo / wiggleplotr
  A small R package to make sequencing read coverage plots in R.
  ☆38Updated 2 years ago
• jrflab / modules
  MSKCC Reis-Filho Lab pipeline thingy
  ☆17Updated 3 weeks ago