Alternatives and similar repositories for Pepper3Dgenome

Users that are interested in Pepper3Dgenome are comparing it to the libraries listed below

• linlabcode / CRC

  View on GitHub
  ☆11May 4, 2021Updated 4 years ago
• yiliao1022 / TADEvoDrosophila

  View on GitHub
  Code for TAD_SV project
  ☆11Mar 16, 2022Updated 3 years ago
• Immortal2333 / Haplotype_Genome_Assembly

  View on GitHub
  Genome haplotype assembly and assessment method
  ☆12Nov 24, 2023Updated 2 years ago
• maiziezhoulab / LRSV_combo

  View on GitHub
  Long Read Based SV Calling Tools Analysis
  ☆14Mar 22, 2024Updated last year
• younglab / CRCmapper

  View on GitHub
  CRCmapper: map core regulatory circuitry
  ☆14Nov 23, 2020Updated 5 years ago
• nbedelman / DiscovarCompGenomics

  View on GitHub
  ☆12Sep 6, 2019Updated 6 years ago
• dwinter / repeatR

  View on GitHub
  read and analyse RepeatMasker output
  ☆27May 22, 2023Updated 2 years ago
• CSOgroup / CALDER

  View on GitHub
  ☆22Jul 27, 2023Updated 2 years ago
• GordonLab / riesling-pipeline

  View on GitHub
  RIESLING: Super-enhancer identification. (Rapid Identification of EnhancerS LInked to Nearby Genes)
  ☆10Jun 28, 2018Updated 7 years ago
• xmliu01 / Uncovering-the-TRN-involved-in-boosting-wheat-regeneration-and-transformation

  View on GitHub
  Code used in article "Uncovering the transcriptional regulatory network involved in boosting wheat regeneration and transformation".
  ☆12Mar 21, 2023Updated 2 years ago
• ajank / balancer-paper

  View on GitHub
  Computational analyses of WGS, mate-pair, RNA-seq, Hi-C and Capture-C data from highly rearranged balancer chromosomes in Drosophila mela…
  ☆10Sep 25, 2019Updated 6 years ago
• YutingPKU / AnalysisPipeline-NGS

  View on GitHub
  ☆12Dec 15, 2020Updated 5 years ago
• Chenghong412 / sheep_introgression

  View on GitHub
  ☆11Sep 1, 2022Updated 3 years ago
• ChrisMaherLab / SV-Hotspot

  View on GitHub
  ☆11May 12, 2021Updated 4 years ago
• T2T-CN1 / CN1

  View on GitHub
  The complete sequence of a Chinese individual
  ☆11Oct 8, 2024Updated last year
• CSOgroup / CALDER2

  View on GitHub
  CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hie…
  ☆26Apr 16, 2025Updated 10 months ago
• jingwanglab / Widespread-linked-selection

  View on GitHub
  Scripts for Wang et al (2020) Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.
  ☆11Feb 15, 2020Updated 6 years ago
• TimothyStephens / Dinoflagellate_Annotation_Workflow

  View on GitHub
  Dinoflagellate Annotation Workflow
  ☆15Oct 3, 2022Updated 3 years ago
• oeco28 / Cacao_Genomics

  View on GitHub
  This is a basic repository with all the scripts necessary to reconstruct the data analysis from our work on the 200 Genomes
  ☆12Aug 31, 2018Updated 7 years ago
• mrvollger / Data-Analysis-for-SDs-in-T2T-CHM13

  View on GitHub
  Figures for the CHM13 T2T SD paper.
  ☆10Sep 12, 2021Updated 4 years ago
• greenelab / tad_pathways_pipeline

  View on GitHub
  Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs
  ☆11Dec 21, 2019Updated 6 years ago
• schneebergerlab / GameteBinning_tetraploid

  View on GitHub
  This is used to achieve haplotype-resolved assembly of tetraploid genomes using gamete sequencings
  ☆12Oct 1, 2021Updated 4 years ago
• linlabbcm / rose2

  View on GitHub
  ☆13Oct 7, 2019Updated 6 years ago
• LingbinNi / soybean_pan-3D_genome_analysis

  View on GitHub
  Pan-3D genome analysis of soybean Hi-C data
  ☆12Mar 6, 2023Updated 2 years ago
• shuzhangcourage / HiC-data-analysis

  View on GitHub
  General analysis of HiC data, including compartment A/B, domains and loops.
  ☆14Feb 17, 2023Updated 3 years ago
• GouXiangJian / SSRMMD

  View on GitHub
  SSRMMD: A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences.
  ☆16Sep 2, 2020Updated 5 years ago
• oushujun / PopTEvo

  View on GitHub
  Study of TE evolution in a population of genomes
  ☆10Dec 11, 2023Updated 2 years ago
• ArimaGenomics / Arima-SV-Pipeline

  View on GitHub
  ☆13Jan 20, 2026Updated 3 weeks ago
• ykai16 / Lollipop

  View on GitHub
  A machine-learning algorithm to predict CTCF-mediated long-range chromatin interactions
  ☆17Nov 7, 2018Updated 7 years ago
• caballero / RepeatLandscape

  View on GitHub
  profile the repeat landscape in a genome
  ☆16Sep 9, 2014Updated 11 years ago
• mdozmorov / RNA-seq

  View on GitHub
  RNA-seq analysis scripts
  ☆16Jan 8, 2026Updated last month
• zlguu / Rice_Heterosis

  View on GitHub
  ☆16Jul 29, 2023Updated 2 years ago
• andreaminio / AnnotationPipeline-EVM_based-DClab

  View on GitHub
  Cantù Lab @ UC Davis - Annotation pipeline - EVM based
  ☆14Nov 1, 2024Updated last year
• 4ureliek / TEorthology

  View on GitHub
  Script to help assessing the evolutionary history of a TE family
  ☆16Sep 5, 2019Updated 6 years ago
• lurebgi / BOPsexChr

  View on GitHub
  Analyses of sex chromosome evolution in songbirds
  ☆16Jun 15, 2019Updated 6 years ago
• getzlab / CPTAC_PanCan_PTM_2023

  View on GitHub
  ☆17Oct 3, 2023Updated 2 years ago
• wlz0726 / Population_Genomics_Scripts

  View on GitHub
  Scripts of population genomics analysis
  ☆36May 8, 2018Updated 7 years ago
• likui345 / PGA

  View on GitHub
  ☆16Jul 25, 2021Updated 4 years ago
• mervesa / HiCDCPlus

  View on GitHub
  HiCDCPlus
  ☆19Jun 6, 2022Updated 3 years ago