Alternatives and similar repositories for Higashi

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

• zhoujt1994 / scHiCluster
  ☆69Updated 3 weeks ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆82Updated last year
• mdozmorov / scHiC_notes
  Notes on single-cell Hi-C technologies, tools, and data
  ☆86Updated last year
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 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
• VRam142 / combinatorialHiC
  Scripts + resources for analyzing combinatorial Hi-C data
  ☆31Updated 6 years ago
• dylkot / pyWNN
  Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)
  ☆19Updated 4 years ago
• JiaqiLiZju / Nvwa
  ☆36Updated 3 years 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
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆92Updated 9 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆100Updated 9 months ago
• yal054 / epiformer
  ☆26Updated 8 months ago
• HYsxe / PRINT
  ☆37Updated last year
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆99Updated 3 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆43Updated 2 months ago
• liu-bioinfo-lab / scHiCTools
  a computational tool for analyzing single cell Hi-C data
  ☆26Updated last year
• buenrostrolab / scPrinter
  ☆56Updated last week
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆66Updated 5 months ago
• gao-lab / Cell_BLAST
  A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
  ☆94Updated last year
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆54Updated last year
• zhaoweiyu-github / ChromBERT
  ChromBERT: A pre-trained foundation model for context-specific transcription regulatory network
  ☆17Updated 2 weeks ago
• SUwonglab / PECA
  PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
  ☆45Updated 2 months ago
• jsxlei / SCALE
  Single-cell ATAC-seq analysis via Latent feature Extraction
  ☆103Updated 2 years ago
• xryanglab / RiboMiner
  a toolset for mining multi-dimensional features of the translatome with ribosome profiling data
  ☆18Updated 5 months ago
• atarashansky / SAMap
  SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.
  ☆85Updated last year
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆113Updated last year
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆53Updated last month
• arnavmdas / epiphany
  ☆12Updated 2 years ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated last year
• hmatsu1226 / SCODE
  SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
  ☆46Updated 6 years ago