Alternatives and similar repositories for MIRA:

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

• 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 2 years ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆60Updated 10 months ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated this week
• HYsxe / PRINT
  ☆35Updated 7 months ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆68Updated 2 weeks ago
• snehamitra / SCARlink
  ☆50Updated 7 months ago
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆41Updated last year
• cantinilab / Circe
  Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).
  ☆21Updated last week
• jcao89757 / TESSA
  Mapping the Functional Landscape of TCR Repertoire
  ☆34Updated 3 years ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆40Updated 3 months ago
• dpeerlab / magic
  MAGIC - imputation and de-noising single-cell RNA seq data sets
  ☆27Updated 5 years ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆67Updated 2 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆71Updated 3 months ago
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆30Updated last month
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆100Updated 7 months ago
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆58Updated last year
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆43Updated 9 months ago
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆72Updated 4 months ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 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
• morris-lab / BiddyetalWorkflow
  This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.
  ☆32Updated 10 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆72Updated last month
• xiaoyeye / TFvelo
  ☆44Updated 11 months ago
• multitalk / awesome-cell-cell-communication
  Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
  ☆45Updated last week
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆57Updated last year
• cailab-tamu / scTenifoldKnk
  R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.
  ☆45Updated 3 months ago
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆49Updated this week
• YosefLab / popV
  ☆73Updated this week
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆28Updated 4 months ago
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆24Updated last month