Alternatives and similar repositories for scDoRI

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

• rs239 / velorama
  Gene regulatory network inference for RNA velocity and pseudotime data
  ☆27Updated 5 months ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆41Updated 8 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆64Updated 2 months ago
• earmingol / scCellFie
  scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.
  ☆36Updated last week
• ajaynadig / TRADEtools
  ☆29Updated 6 months ago
• mvinyard / ArchR-h5ad
  Parse ArchR arrow files to anndata h5ad
  ☆14Updated last year
• settylab / Mellon
  Non-parametric density inference for single-cell analysis.
  ☆72Updated 3 months ago
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆49Updated 7 months ago
• theislab / cross_system_integration
  ☆13Updated last week
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆30Updated 2 years ago
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆28Updated this week
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆55Updated 3 months ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆87Updated 3 months ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 4 months ago
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆34Updated 6 months ago
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆53Updated last year
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆79Updated 5 months ago
• decomverse / ACTIONet
  ACTIONet single-cell analysis framework
  ☆42Updated 11 months ago
• loosolab / scanpro
  A modular tool for proportion analysis in single-cell sequencing data
  ☆23Updated this week
• CostaLab / scMEGA
  scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
  ☆40Updated 11 months ago
• netbiolab / scHumanNet
  Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3
  ☆43Updated last week
• azizilab / decipher
  A single-cell analysis toolkit to jointly analyze samples from distinct conditions
  ☆32Updated 5 months ago
• bendemeo / shannonca
  Information-based dimensionality reduction
  ☆29Updated 9 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆64Updated last week
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆54Updated last year
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 3 years ago
• doraadong / TraSig
  Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data
  ☆25Updated 2 years ago
• forrest-lab / NATMI
  NATMI: Network Analysis Toolkit for the Multicellular Interactions
  ☆35Updated 4 years ago
• bowang-lab / DeepVelo
  ☆46Updated last year
• swaruplabUCI / DSAD_Spatial_Miyoshi_Morabito_2024
  Code associated with the data analysis for Miyoshi & Morabito 2024
  ☆23Updated 2 months ago