jzhoulab / orca

Related projects ⓘ

Alternatives and complementary repositories for orca

• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆66Updated 4 months ago
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆78Updated last month
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆54Updated last year
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆92Updated last year
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆59Updated 6 months ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆121Updated 2 months ago
• Papatheodorou-Group / BENGAL
  Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets
  ☆33Updated 7 months ago
• aertslab / arboreto
  A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
  ☆52Updated 7 months ago
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆46Updated 4 months ago
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆77Updated 3 weeks ago
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated 5 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆110Updated 2 months ago
• ShobiStassen / VIA
  trajectory inference
  ☆86Updated last month
• YosefLab / Cassiopeia
  A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
  ☆80Updated last week
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆108Updated this week
• bowang-lab / DeepVelo
  ☆46Updated 9 months ago
• lhqing / ALLCools
  Toolkit for single-cell DNA methylation analysis.
  ☆39Updated last week
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆59Updated 7 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆107Updated 2 weeks ago
• single-cell-genetics / cellsnp-lite
  Efficient genotyping bi-allelic SNPs on single cells
  ☆131Updated 4 months ago
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆66Updated 3 months ago
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆96Updated 9 months ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆84Updated this week
• wukevin / babel
  Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
  ☆38Updated last year
• gao-lab / Cell_BLAST
  A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
  ☆86Updated 3 months ago
• rnakato / ShortCake
  A docker image for single-cell analysis
  ☆66Updated 5 months ago
• KlugerLab / ALRA
  Imputation method for scRNA-seq based on low-rank approximation
  ☆73Updated 10 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆89Updated this week
• arnavmdas / epiphany
  ☆10Updated last year
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆30Updated this week