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 3 years ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆50Updated 7 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆123Updated 2 weeks ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last month
• KlugerLab / ALRA
  Imputation method for scRNA-seq based on low-rank approximation
  ☆77Updated last year
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆41Updated 11 months ago
• jcao89757 / TESSA
  Mapping the Functional Landscape of TCR Repertoire
  ☆35Updated 4 years ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆91Updated 6 months ago
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆49Updated last year
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆29Updated this week
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆42Updated this week
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆78Updated 2 months ago
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆97Updated 11 months ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆44Updated 2 years ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆107Updated 2 years ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆77Updated 9 months ago
• forrest-lab / NATMI
  NATMI: Network Analysis Toolkit for the Multicellular Interactions
  ☆35Updated 4 years ago
• wycwycpku / RSCORE
  ☆27Updated 4 years ago
• snehamitra / SCARlink
  ☆59Updated 5 months ago
• HYsxe / PRINT
  ☆37Updated last year
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆113Updated last year
• Papatheodorou-Group / BENGAL
  Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets
  ☆41Updated 4 months ago
• ggjlab / HCL
  Tools used in Human Cell Landscape(HCL)
  ☆56Updated 5 years ago
• kunwang34 / PhyloVelo
  PhyloVelo, Phylogeny-based transcriptomic velocity of single cells
  ☆43Updated 2 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆80Updated 10 months ago
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆71Updated last year
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆62Updated last year
• morris-lab / BiddyetalWorkflow
  This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.
  ☆32Updated last year
• neocaleb / TENET
  TENET is a tool for reconstructing gene regulatory networks from pseudo-time ordered single-cell transcriptomic data.
  ☆41Updated 3 years ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆44Updated 3 months ago