Alternatives and similar repositories for InSituType

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

• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆77Updated 3 years ago
• jbergenstrahle / STUtility
  ☆52Updated 2 years ago
• single-cell-genetics / XClone
  Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.
  ☆36Updated last week
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆84Updated last month
• rajewsky-lab / spacemake
  ☆44Updated last week
• JEFworks-Lab / veloviz
  RNA-velocity informed embeddings for visualizing cellular trajectories
  ☆43Updated 2 years ago
• pachterlab / LP_2021
  ☆49Updated 3 weeks ago
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆61Updated last year
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆105Updated this week
• pachterlab / voyager
  From geospatial to spatial -omics
  ☆95Updated 4 months ago
• saeyslab / spotless-benchmark
  A repository for benchmarking spatial deconvolution and mapping tools
  ☆33Updated 2 months ago
• JCVenterInstitute / NSForest
  A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…
  ☆63Updated 2 weeks ago
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆53Updated last month
• PMBio / MuDataSeurat
  .h5mu files interface for Seurat
  ☆32Updated last year
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆33Updated last month
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆32Updated last year
• alexisvdb / singleCellHaystack
  Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
  ☆83Updated 10 months ago
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆53Updated 10 months ago
• Nanostring-Biostats / CosMx-Analysis-Scratch-Space
  This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…
  ☆71Updated this week
• jfnavarro / st_analysis
  A toolset for analysis and visualisation of Spatial Transcriptomics datasets.
  ☆18Updated 4 years ago
• Nanostring-Biostats / SpatialDecon
  The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…
  ☆39Updated last month
• swaruplabUCI / ArchRtoSignac
  An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
  ☆36Updated 10 months ago
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆100Updated 2 months ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆42Updated 2 years ago
• maggiecrow / MetaNeighbor
  ☆49Updated 7 years ago
• klarman-cell-observatory / hdst
  ☆19Updated 5 years ago
• colomemaria / epiAneufinder
  R package to detect breakpoints and assign somies to scATAC-seq data
  ☆40Updated last month
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆83Updated last month
• lcmmichielsen / scHPL
  ☆35Updated 4 months ago
• atarashansky / self-assembling-manifold
  The Self-Assembling-Manifold (SAM) algorithm.
  ☆42Updated 11 months ago