Alternatives and similar repositories for mfishtools

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

• vitessce / vitessceR
  R API and htmlwidget for Vitessce
  ☆43Updated 3 months ago
• korsunskylab / rcna
  R implementation of the Reshef and Rumker CNA method (https://github.com/immunogenomics/cna)
  ☆15Updated 2 years ago
• pachterlab / concordexR
  Compute the neighborhood consolidation matrix and identify SHRs
  ☆13Updated 5 months ago
• drighelli / SpatialExperiment
  ☆71Updated 5 months ago
• AllenInstitute / scrattch
  Single cell RNA-seq analysis for transcriptomic type characterization
  ☆37Updated 2 months ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆30Updated last year
• maggiecrow / MetaNeighbor
  ☆48Updated 7 years ago
• pachterlab / SpatialFeatureExperiment
  Extension of SpatialExperiment with sf
  ☆55Updated 2 weeks ago
• greenelab / miQC
  Flexible, probablistic metrics for quality control of scRNA-seq data
  ☆21Updated 2 years ago
• msraredon / Connectome
  ☆30Updated 3 years ago
• saezlab / MOFAcellulaR
  R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)
  ☆11Updated 2 years ago
• JCVenterInstitute / FRmatch
  Cell type matching in single-cell RNA-sequencing data using FR-Match
  ☆19Updated 2 months ago
• const-ae / transformGamPoi
  Variance stabilizing transformation for Gamma Poisson distributed data
  ☆22Updated 2 years ago
• quadbio / VoxHunt
  VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
  ☆47Updated last year
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆16Updated 2 months ago
• gdagstn / borges
  Antique or modern atlas-like depictions of non-linear dimensionality reduction for single cell data
  ☆18Updated 5 months ago
• ChristophH / in-lineage
  Data and code for the paper "Developmental diversification of cortical inhibitory interneurons"
  ☆24Updated 6 years ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆37Updated 5 months ago
• zdebruine / singlet
  Single-cell analysis with non-negative matrix factorization
  ☆45Updated 3 months ago
• saeyslab / FlowSOM
  Using self-organizing maps for visualization and interpretation of cytometry data
  ☆29Updated this week
• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆52Updated last year
• saeyslab / spotless-benchmark
  A repository for benchmarking spatial deconvolution and mapping tools
  ☆35Updated 6 months ago
• MSingerLab / COMETSC
  COMET Single-Cell Marker Detection tool
  ☆31Updated 3 years ago
• AllenInstitute / tasic2018analysis
  Scripts related to VISp and ALM scRNA-seq and FISH analysis for Tasic, et al., 2018.
  ☆24Updated 7 years ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆43Updated 6 months ago
• SydneyBioX / scFeatures
  ☆14Updated last month
• single-cell-genetics / XClone
  Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.
  ☆38Updated this week
• lmweber / diffcyt
  R package for differential discovery analyses in high-dimensional cytometry data
  ☆21Updated 9 months ago
• SydneyBioX / MoleculeExperiment
  ☆12Updated last year
• davemcg / scEiaD
  Snakefile-based process to turn 1.4 million ocular cells into a unified meta-atlas
  ☆26Updated last year