Alternatives and similar repositories for sci

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

• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆86Updated 10 months ago
• liu-bioinfo-lab / scHiCTools
  a computational tool for analyzing single cell Hi-C data
  ☆25Updated 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
• VRam142 / combinatorialHiC
  Scripts + resources for analyzing combinatorial Hi-C data
  ☆30Updated 5 years ago
• ma-compbio / MATCHA
  multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learning
  ☆29Updated 3 years ago
• JinLabBioinfo / HiCorr
  HiCorr: a Hi-C data bias-correction pipeline
  ☆28Updated 4 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆77Updated last year
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆106Updated 2 years ago
• mdozmorov / scHiC_notes
  Notes on single-cell Hi-C technologies, tools, and data
  ☆80Updated 9 months ago
• zhoujt1994 / scHiCluster
  ☆67Updated 2 months ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆89Updated 5 months ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated 8 months ago
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆73Updated last year
• Maarten-vd-Sande / qnorm
  Fast-ish (and correct!) quantile normalization in Python.
  ☆31Updated 2 months ago
• open2c / cooler-binder
  Cooler demo using a Jupyter notebook Binder
  ☆18Updated 4 years ago
• JinLabBioinfo / DeepLoop
  DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data
  ☆32Updated 4 months ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆128Updated 6 months ago
• GuanLab / Anchor
  This is the package of Yuanfang's winning algorithm in the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge
  ☆20Updated 5 years ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆97Updated 5 months ago
• SUwonglab / PECA
  PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
  ☆44Updated last year
• hms-dbmi / 3d-genome-processing-tutorial
  A 3D genome data processing tutorial for ISMB/ECCB 2017
  ☆50Updated 8 years ago
• jsxlei / SCALE
  Single-cell ATAC-seq analysis via Latent feature Extraction
  ☆102Updated last year
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆97Updated 8 months ago
• rschwess / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆9Updated 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…
  ☆64Updated 2 years ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆44Updated 8 months ago
• openvax / gtfparse
  Parsing tools for GTF (gene transfer format) files
  ☆121Updated 5 months ago
• mdozmorov / ChIP-seq_notes
  Notes on ChIP-seq and other-seq-related tools
  ☆26Updated 3 weeks ago
• BogdanBintu / ChromatinImaging
  Super-resolution chromatin tracing 2018
  ☆16Updated 4 years ago