Alternatives and similar repositories for MoleculeExperiment

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

• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆14Updated last month
• pachterlab / concordexR
  Compute the neighborhood consolidation matrix and identify SHRs
  ☆13Updated last week
• const-ae / pyLemur
  A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
  ☆25Updated 5 months ago
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 5 months ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆32Updated 2 weeks ago
• saezlab / MOFAcellulaR
  R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)
  ☆11Updated last year
• wanglab-broad / CAST
  CAST package
  ☆40Updated 7 months ago
• Teichlab / sctk
  ☆39Updated 8 months ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆27Updated 8 months ago
• damienArnol / svca
  ☆13Updated 6 years ago
• saeyslab / spotless-benchmark
  A repository for benchmarking spatial deconvolution and mapping tools
  ☆33Updated last month
• satijalab / panhumanpy
  ☆17Updated last month
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆29Updated 7 months ago
• PMBio / SpatialDE
  Test genes for Spatial Variation
  ☆14Updated 6 months ago
• greenelab / miQC
  Flexible, probablistic metrics for quality control of scRNA-seq data
  ☆20Updated 2 years ago
• loosolab / scanpro
  A modular tool for proportion analysis in single-cell sequencing data
  ☆22Updated last month
• vitessce / vitessceR
  R API and htmlwidget for Vitessce
  ☆40Updated 8 months ago
• bhuvad / SpaNorm
  R package for normalisation of spatial transcriptomics data
  ☆10Updated last week
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 2 months ago
• CamaraLab / STvEA
  Spatially-resolved Transcriptomics via Epitope Anchoring
  ☆19Updated last year
• almaan / eggplant
  ☆22Updated 2 years ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆23Updated 10 months ago
• MarioniLab / StabMap
  Mosaic single cell data integration using non-overlapping features
  ☆37Updated 2 years ago
• Teichlab / visium_stitcher
  Stitch multiple Visium slides together
  ☆16Updated last year
• dissatisfaction-ai / scHierarchy
  A toolking for cell type hierarchies: marker selection & consistent classification
  ☆22Updated last year
• 10XGenomics / janesick_nature_comms_2023_companion
  Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spat…
  ☆23Updated last year
• ventolab / cellphonedbviz
  Interactive visualisation of CellphoneDB results
  ☆10Updated 5 months ago
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆32Updated last year
• FridleyLab / spatialGE
  Methods for visualization and analysis of spatially-resolved gene expression
  ☆20Updated 3 weeks ago
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆27Updated 11 months ago