visium
There are 20 repositories under visium topic.
broadinstitute/Tangram
Spatial alignment of single cell transcriptomic data.
LieberInstitute/spatialLIBD
Code for the spatialLIBD R/Bioconductor package and shiny app
LieberInstitute/HumanPilot
Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project
jfnavarro/st_pipeline
ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
nf-core/spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
ismms-himc/visium-clustergrammer2
Spatial Transcriptomics Dashboard
HaojiaWu/CellScopes.jl
A Julia package for single cell and spatial data analysis
lima1/sttkit
Pipeline for SpatialTranscriptomics and 10X Visium data
LieberInstitute/spatialDLPFC
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
LieberInstitute/VistoSeg
Image processing pipeline for spatial projects
10XGenomics/janesick_nature_comms_2023_companion
Code 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"
TheJacksonLaboratory/STQ
Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
neuhausi/canvasxpress-js
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
gustaveroussy/CFS
R package using ICA based method for spatial transcriptomics analysis (Visium/Slide-seq/CosMX/MERSCOPE)
TheHumphreysLab/CellScopes.jl
A Julia package for single cell and spatial data analysis
gurbaaz27/cs690a-clustering-spatial-transcriptomics-data
Course Assignment on Clustering of Spatial Transcriptomics Data
LieberInstitute/Visium_SPG_AD
Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.
LieberInstitute/visiumStitched
R package containing functions useful for stitching Visium capture areas. Related to the example human brain data described at http://research.libd.org/visiumStitched_brain/.
OlivierRaineteauSBRI/scRNASeq
Repo linked to our recent publication in Science Advances
LieberInstitute/visiumStitched_brain
Example human brain data used for https://research.libd.org/visiumStitched/.