Alternatives and similar repositories for Higashi

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

• zhoujt1994 / scHiCluster
  ☆69Updated last month
• mdozmorov / scHiC_notes
  Notes on single-cell Hi-C technologies, tools, and data
  ☆86Updated last year
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆82Updated last year
• dylkot / pyWNN
  Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)
  ☆19Updated 4 years ago
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated last year
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆44Updated 3 months ago
• buenrostrolab / scPrinter
  ☆57Updated 3 weeks ago
• yal054 / epiformer
  ☆26Updated 8 months ago
• VRam142 / combinatorialHiC
  Scripts + resources for analyzing combinatorial Hi-C data
  ☆31Updated 6 years ago
• JiaqiLiZju / Nvwa
  ☆36Updated 3 years ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆92Updated 10 months ago
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆71Updated 2 years ago
• liu-bioinfo-lab / scHiCTools
  a computational tool for analyzing single cell Hi-C data
  ☆26Updated last year
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆67Updated 6 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆110Updated 3 years ago
• aertslab / CREsted
  CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…
  ☆55Updated 2 weeks ago
• HYsxe / PRINT
  ☆37Updated last year
• jsxlei / SCALE
  Single-cell ATAC-seq analysis via Latent feature Extraction
  ☆103Updated 2 years ago
• SUwonglab / PECA
  PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
  ☆45Updated 3 months ago
• lhqing / ALLCools
  Toolkit for single-cell DNA methylation analysis.
  ☆45Updated last month
• Papatheodorou-Group / BENGAL
  Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets
  ☆42Updated 5 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆100Updated 10 months ago
• josephreplogle / guide_calling
  Tools for sgRNA calling in direct capture Perturb-seq data
  ☆39Updated 2 years ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆53Updated 2 months ago
• zhaoweiyu-github / ChromBERT
  ChromBERT: A pre-trained foundation model for context-specific transcription regulatory network
  ☆17Updated last week
• gao-lab / Cell_BLAST
  A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
  ☆94Updated last year
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆30Updated 2 months ago
• karbalayghareh / GraphReg
  Chromatin interaction aware gene regulatory modeling with graph attention networks
  ☆28Updated 2 years ago
• kunwang34 / PhyloVelo
  PhyloVelo, Phylogeny-based transcriptomic velocity of single cells
  ☆43Updated 3 months ago
• beyondpie / CEMBA_wmb_snATAC
  Whole mouse brain snATAC seq analysis
  ☆28Updated 8 months ago