Alternatives and similar repositories for mfishtools

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

• pachterlab / concordexR
  Compute the neighborhood consolidation matrix and identify SHRs
  ☆13Updated last month
• korsunskylab / rcna
  R implementation of the Reshef and Rumker CNA method (https://github.com/immunogenomics/cna)
  ☆15Updated last year
• AllenInstitute / scrattch
  Single cell RNA-seq analysis for transcriptomic type characterization
  ☆37Updated this week
• vitessce / vitessceR
  R API and htmlwidget for Vitessce
  ☆42Updated this week
• drighelli / SpatialExperiment
  ☆66Updated 2 months ago
• msraredon / Connectome
  ☆28Updated 3 years ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆27Updated 10 months ago
• bdsc-tds / SPLIT
  Profile purification of single-cell spatial transcriptomics data
  ☆14Updated 3 weeks ago
• quadbio / VoxHunt
  VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
  ☆46Updated last year
• const-ae / transformGamPoi
  Variance stabilizing transformation for Gamma Poisson distributed data
  ☆22Updated 2 years ago
• saezlab / MOFAcellulaR
  R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)
  ☆11Updated last year
• greenelab / miQC
  Flexible, probablistic metrics for quality control of scRNA-seq data
  ☆20Updated 2 years ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆35Updated last month
• JCVenterInstitute / FRmatch
  Cell type matching in single-cell RNA-sequencing data using FR-Match
  ☆19Updated 4 months ago
• maggiecrow / MetaNeighbor
  ☆49Updated 7 years ago
• saeyslab / brainimmuneatlas
  Overview of the scripts used to analyse the brainimmuneatlas data
  ☆19Updated 4 years ago
• ChristophH / in-lineage
  Data and code for the paper "Developmental diversification of cortical inhibitory interneurons"
  ☆24Updated 6 years ago
• SydneyBioX / scClassify
  Hierarchical classification of cells
  ☆25Updated last year
• saeyslab / spotless-benchmark
  A repository for benchmarking spatial deconvolution and mapping tools
  ☆33Updated 2 months ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆38Updated 2 months ago
• pachterlab / SpatialFeatureExperiment
  Extension of SpatialExperiment with sf
  ☆55Updated last month
• AllenInstitute / tasic2018analysis
  Scripts related to VISp and ALM scRNA-seq and FISH analysis for Tasic, et al., 2018.
  ☆23Updated 7 years ago
• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆51Updated last year
• zdebruine / singlet
  Single-cell analysis with non-negative matrix factorization
  ☆45Updated 2 weeks ago
• mojaveazure / loomR
  An R-based interface for loom files
  ☆66Updated 5 years ago
• saeyslab / FlowSOM
  Using self-organizing maps for visualization and interpretation of cytometry data
  ☆29Updated last week
• pachterlab / BHGP_2022
  ☆21Updated 3 years ago
• davemcg / scEiaD
  Snakefile-based process to turn 1.4 million ocular cells into a unified meta-atlas
  ☆26Updated last year
• Elisseeff-Lab / domino
  A software package for connecting cell level features in single cell RNA sequencing data with receptor ligand activity. Please be aware t…
  ☆17Updated 8 months ago
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆30Updated 8 months ago