Alternatives and similar repositories for HiCFoundation

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

• Illumina / PromoterAI
  ☆78Updated 3 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆43Updated 2 weeks ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆79Updated last year
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆96Updated 7 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆77Updated last month
• liu-bioinfo-lab / EPCOT
  ☆24Updated last year
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆89Updated last year
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆68Updated 2 years ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated 10 months ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆92Updated 7 months ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆22Updated last month
• VRam142 / combinatorialHiC
  Scripts + resources for analyzing combinatorial Hi-C data
  ☆31Updated 5 years ago
• BGIResearch / BioLLM
  ☆27Updated 5 months ago
• HelloWorldLTY / UKBioLM
  ☆21Updated 5 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆64Updated 6 months ago
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆92Updated last month
• epigen / CellWhisperer
  CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets
  ☆62Updated 11 months ago
• karbalayghareh / GraphReg
  Chromatin interaction aware gene regulatory modeling with graph attention networks
  ☆27Updated 2 years ago
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆35Updated 6 months ago
• SuperBianC / scMulan
  Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
  ☆60Updated last year
• b2jia / jie
  A spatial genome aligner for analyzing multiplexed DNA-FISH imaging data.
  ☆18Updated last year
• xiongxslab / Translatomer
  ☆24Updated last month
• biagent-dev / bia
  BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow
  ☆38Updated last year
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated last year
• mostafavilabuw / EnformerAssessment
  ☆24Updated last year
• jzhoulab / puffin_manuscript
  ☆17Updated 11 months ago
• zhoujt1994 / scHiCluster
  ☆68Updated 4 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆47Updated this week
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆30Updated 8 months ago