Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: visium
TheJacksonLaboratory/STQ
Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
Language: Python - Size: 3.54 MB - Last synced: about 2 hours ago - Pushed: about 14 hours ago - Stars: 9 - Forks: 0
LieberInstitute/spatialDLPFC
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
Language: HTML - Size: 14.9 GB - Last synced: about 4 hours ago - Pushed: about 17 hours ago - Stars: 10 - Forks: 0
gustaveroussy/CFS
R package using ICA based method for spatial transcriptomics analysis (Visium/Slide-seq/CosMX/MERSCOPE)
Language: R - Size: 21.8 MB - Last synced: about 19 hours ago - Pushed: 2 days ago - Stars: 6 - Forks: 2
neuhausi/canvasxpress-js
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
Language: CSS - Size: 25.7 MB - Last synced: about 13 hours ago - Pushed: 1 day ago - Stars: 8 - Forks: 1
TheHumphreysLab/CellScopes.jl Fork of HaojiaWu/CellScopes.jl
A Julia package for single cell and spatial data analysis
Language: Julia - Size: 126 MB - Last synced: about 16 hours ago - Pushed: 1 day ago - Stars: 5 - Forks: 1
HaojiaWu/CellScopes.jl
A Julia package for single cell and spatial data analysis
Language: Julia - Size: 126 MB - Last synced: about 18 hours ago - Pushed: 1 day ago - Stars: 17 - Forks: 2
lima1/sttkit
Pipeline for SpatialTranscriptomics and 10X Visium data
Language: R - Size: 541 KB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 19 - Forks: 7
LieberInstitute/spatialLIBD
Code for the spatialLIBD R/Bioconductor package and shiny app
Language: R - Size: 187 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 72 - Forks: 15
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.
Language: HTML - Size: 2.09 GB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 0
nf-core/spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Language: Nextflow - Size: 6.94 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 39 - Forks: 12
broadinstitute/Tangram
Spatial alignment of single cell transcriptomic data.
Language: Jupyter Notebook - Size: 141 MB - Last synced: 17 days ago - Pushed: 9 months ago - Stars: 220 - Forks: 45
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"
Language: Jupyter Notebook - Size: 7.91 MB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 7 - Forks: 0
OlivierRaineteauSBRI/scRNASeq
Repo linked to our recent publication in Science Advances
Language: HTML - Size: 5.66 GB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0
LieberInstitute/HumanPilot
Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project
Language: HTML - Size: 289 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 55 - Forks: 27
LieberInstitute/VistoSeg
Image processing pipeline for spatial projects
Language: MATLAB - Size: 312 MB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 14 - Forks: 3
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.
Language: Python - Size: 144 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 45 - Forks: 43
gurbaaz27/cs690a-clustering-spatial-transcriptomics-data
Course Assignment on Clustering of Spatial Transcriptomics Data
Language: Jupyter Notebook - Size: 62.2 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 4 - Forks: 0
ismms-himc/visium-clustergrammer2
Spatial Transcriptomics Dashboard
Language: Jupyter Notebook - Size: 29 MB - Last synced: 12 months ago - Pushed: over 4 years ago - Stars: 25 - Forks: 3
