Alternatives and similar repositories for MRtree

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

• BrainStOrmics / Spaco
  Spatially constrained color profiling for visualizing single-cell resolution spatial data
  ☆25Updated last year
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆17Updated 4 months ago
• loosolab / scanpro
  A modular tool for proportion analysis in single-cell sequencing data
  ☆24Updated 4 months ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆48Updated 8 months ago
• DavisLaboratory / scDECAF
  Querying cellular states and programs by learning representations of gene sets
  ☆15Updated 3 months ago
• AllenInstitute / scrattch
  Single cell RNA-seq analysis for transcriptomic type characterization
  ☆38Updated 4 months ago
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 4 months ago
• single-cell-genetics / XClone
  Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.
  ☆38Updated 2 weeks ago
• davemcg / scEiaD
  Snakefile-based process to turn 1.4 million ocular cells into a unified meta-atlas
  ☆26Updated 2 years ago
• saeyslab / brainimmuneatlas
  Overview of the scripts used to analyse the brainimmuneatlas data
  ☆19Updated 5 years ago
• Teichlab / sctk
  ☆45Updated 2 weeks ago
• JEFworks-Lab / veloviz
  RNA-velocity informed embeddings for visualizing cellular trajectories
  ☆44Updated 3 years ago
• MagpiePKU / EpiTrace
  Cell age determination by scATAC-seq and bulk-ATAC-seq
  ☆32Updated last week
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆65Updated this week
• PMBio / MuDataSeurat
  .h5mu files interface for Seurat
  ☆32Updated 2 years ago
• jfnavarro / st_analysis
  A toolset for analysis and visualisation of Spatial Transcriptomics datasets.
  ☆18Updated 4 years ago
• dyxmvp / Spatial_ATAC-seq
  ☆23Updated 2 years ago
• SydneyBioX / scFeatures
  ☆14Updated 2 weeks ago
• rbpatt2019 / chooseR
  An R framework for choosing clustering parameters in scRNA-seq analysis pipelines
  ☆36Updated 5 years ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆24Updated 2 years ago
• SydneyBioX / MoleculeExperiment
  ☆12Updated last year
• quadbio / VoxHunt
  VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
  ☆47Updated last year
• saezlab / MOFAcellulaR
  R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)
  ☆12Updated 2 years ago
• gerstung-lab / BaSISS
  Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
  ☆27Updated 3 years ago
• saeyslab / spotless-benchmark
  A repository for benchmarking spatial deconvolution and mapping tools
  ☆36Updated 8 months ago
• wanglab-broad / CAST
  CAST package
  ☆42Updated last year
• bendemeo / shannonca
  Information-based dimensionality reduction
  ☆29Updated last year
• hsmaan / Iniquitate
  Analysis of imbalanced data and its impacts in a scRNA-seq integration setting
  ☆31Updated 11 months ago
• AllenInstitute / scrattch.bigcat
  iterative clustering pipeline of big single cell datasets.
  ☆36Updated 5 months ago
• theislab / troutpy
  Package for the analysis of Transcripts outside segmented cells in ST data
  ☆26Updated this week