Alternatives and similar repositories for DeepLoop

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

• JinLabBioinfo / HiCorr
  HiCorr: a Hi-C data bias-correction pipeline
  ☆28Updated 5 months ago
• joachimwolff / scHiCExplorer
  Single-cell Hi-C data analysis toolbox
  ☆27Updated 4 years ago
• HuMingLab / SnapHiC
  SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data
  ☆41Updated 2 years ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year
• YaqiangCao / cLoops2
  Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
  ☆48Updated 2 months ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆68Updated last year
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆69Updated 10 months ago
• XiaoTaoWang / Best-Labs-of-3D-Genome
  Data and the co-authored network I extracted for lab selection in 3D genome research field
  ☆15Updated 3 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆39Updated 4 years ago
• ma-compbio / Fast-Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition
  ☆19Updated 2 years ago
• ay-lab / FitHiChIP
  Statistically Significant loops from HiChIP data
  ☆44Updated last year
• vierstralab / motif-clustering
  Clustering motif models to remove redundancy
  ☆42Updated 2 years ago
• GuipengLi / ChIA-PET2
  a versatile and flexible pipeline for analysing different variants of ChIA-PET data
  ☆34Updated 9 months ago
• zsq-berry / 3D-genome-tools
  ☆12Updated 3 years ago
• wangjuan001 / hicplus
  ☆12Updated 4 years ago
• bernardo-de-almeida / motif-clustering
  Clustering TF motif models from multiple species (mostly focused on Drosophila and human) by similarity to remove redundancy
  ☆27Updated 2 years ago
• dbrg77 / scATAC_snakemake
  Snakemake pipeline for plate scATAC-seq processing
  ☆26Updated last year
• ernstlab / full_stack_ChromHMM_annotations
  Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes
  ☆37Updated last year
• zhoujt1994 / scHiCluster
  ☆68Updated 3 months ago
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated last year
• huyustats / SCATS
  A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
  ☆22Updated 2 years ago
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆74Updated last month
• open2c / open2c_examples
  ☆17Updated last year
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆74Updated last year
• ma-compbio / scGHOST
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment
  ☆20Updated last year
• open2c / cooler-binder
  Cooler demo using a Jupyter notebook Binder
  ☆18Updated 4 years ago
• JiaqiLiZju / Nvwa
  ☆35Updated 2 years ago
• paulsengroup / hictkpy
  Python bindings for hictk: read and write .cool and .hic files directly from Python
  ☆15Updated last week
• ysora / stripenn
  Architectural stripe detection from 3D genome conformation data
  ☆18Updated 2 years ago