Alternatives and similar repositories for cytopus

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

• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆99Updated last year
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆69Updated 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
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆69Updated 2 months ago
• snehamitra / SCARlink
  ☆61Updated last month
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆41Updated last year
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆71Updated 2 years ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆67Updated 6 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆79Updated 10 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆83Updated 9 months ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆94Updated 7 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆126Updated last month
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆49Updated last year
• SchubertLab / mvTCR
  ☆56Updated last year
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆78Updated 3 weeks ago
• buenrostrolab / stimATAC_analyses_code
  All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs
  ☆41Updated 2 years ago
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆80Updated 5 months ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆29Updated last year
• bowang-lab / DeepVelo
  ☆47Updated last year
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆105Updated last year
• theislab / regvelo
  inferring regulatory cellular dynamics
  ☆61Updated 3 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆113Updated last year
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆62Updated last year
• settylab / Mellon
  Non-parametric density inference for single-cell analysis.
  ☆74Updated 7 months ago
• xiaoyeye / TFvelo
  ☆46Updated last year
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆45Updated 4 months ago
• kunwang34 / PhyloVelo
  PhyloVelo, Phylogeny-based transcriptomic velocity of single cells
  ☆43Updated 3 months ago
• morris-lab / BiddyetalWorkflow
  This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.
  ☆32Updated last year
• omnideconv / omnideconv
  Unified access to several second-generation deconvolution methods
  ☆88Updated last week
• vibscc / DALI
  R-package for the analysis of single-cell TCR/BCR data in the Seurat ecosystem
  ☆20Updated 9 months ago