50 skills found · Page 1 of 2
broadinstitute / TangramSpatial alignment of single cell transcriptomic data.
gustaveroussy / SopaTechnology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
Teichlab / Bin2cellJoin subcellular Visium HD bins into cells
10XGenomics / HumanColonCancer VisiumHDAssociated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"
LieberInstitute / SpatialLIBDCode for the spatialLIBD R/Bioconductor package and shiny app
saezlab / Visium HeartSpatial transcriptomics of heart tissue
LieberInstitute / HumanPilotSpatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project
jfnavarro / St PipelineST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
aerickso / SpatialInferCNVClone Calling from Visium Spatial Transcriptomics of Cancer samples
Sanofi-Public / Enact PipelineRepository for ENACT pipeline for end-to-end analysis of Visium HD data
nf-core / SpatialviPipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
ratschlab / DeepSpotDeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xenium) resolution.
HaojiaWu / CellScopes.jlA Julia package for single cell and spatial data analysis
camlab-bioml / RakaiaInteractive spatial omics viewer in the browser for thousands of images | https://rakaia.io/
lfranzen / Spatial Lung FibrosisRepository for all R scripts used for the bioinformatic analyses of the mouse and human 10x Genomics Visium spatially resolved transcriptomics data presented in our associated manuscript.
LieberInstitute / SpatialDLPFCspatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
10XGenomics / Janesick Nature Comms 2023 CompanionCode companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue"
ismms-himc / Visium Clustergrammer2Spatial Transcriptomics Dashboard
TheJacksonLaboratory / STQSpatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
lima1 / SttkitPipeline for SpatialTranscriptomics and 10X Visium data
