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
• snehamitra / SCARlink
  ☆54Updated this week
• HYsxe / PRINT
  ☆35Updated 9 months ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆68Updated this week
• dpeerlab / magic
  MAGIC - imputation and de-noising single-cell RNA seq data sets
  ☆27Updated 5 years ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆60Updated last year
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆41Updated 2 years ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 2 months ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆41Updated 5 months ago
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆59Updated last year
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆102Updated 9 months ago
• morris-lab / BiddyetalWorkflow
  This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.
  ☆32Updated last year
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆45Updated 11 months ago
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆79Updated 6 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆71Updated 4 months ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆43Updated 3 years ago
• theislab / regvelo
  inferring regulatory cellular dynamics
  ☆48Updated last week
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆32Updated 3 months ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆42Updated 2 years ago
• liulab-dfci / lisa2
  ☆30Updated 2 years ago
• jcao89757 / TESSA
  Mapping the Functional Landscape of TCR Repertoire
  ☆34Updated 3 years ago
• kunwang34 / PhyloVelo
  PhyloVelo, Phylogeny-based transcriptomic velocity of single cells
  ☆43Updated last year
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆25Updated 3 weeks ago
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆69Updated last year
• forrest-lab / NATMI
  NATMI: Network Analysis Toolkit for the Multicellular Interactions
  ☆34Updated 4 years ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆102Updated last year
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 2 months ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆82Updated last month
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 2 months ago
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆62Updated 3 years ago