Topic: spatial-transcriptomics Goto Github

👇 Here are 147 public repositories matching this topic...

10xgenomics / humancoloncancer_visiumhd
spatial-transcriptomics,Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"
Organization: 10xgenomics
Home Page: https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression
spatial-transcriptomics visiumhd

acycliq / pciseq
spatial-transcriptomics,A probabilistic cell typing algorithm for spatial transcriptomics.
User: acycliq
neuroscience spatial-transcriptomics

alexisvdb / singlecellhaystack
spatial-transcriptomics,Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
User: alexisvdb
Home Page: https://alexisvdb.github.io/singleCellHaystack/
bioinformatics single-cell r transcriptomics spatial-transcriptomics cite-seq pseudotime scatac-seq spatial-proteomics

altschulerwu-lab / muse
spatial-transcriptomics,MUSE is a deep learning approach characterizing tissue composition through combined analysis of morphologies and transcriptional states for spatially resolved transcriptomics data.
Organization: altschulerwu-lab
single-cell-ananlysis deep-learning multi-modal-analysis data-integration spatial-transcriptomics tensorflow clustering

aristoteleo / spateo-release
spatial-transcriptomics,Spatiotemporal modeling of spatial transcriptomics
Organization: aristoteleo
Home Page: https://spateo-release.readthedocs.io/
3d-reconstruction cell-segmentation spatial-transcriptomics spatiotemporal

ccruizm / gbmap
spatial-transcriptomics,Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.
User: ccruizm
cell-cell-communication glioblastoma large-scale-data-analytics single-cell-rna-seq spatial-transcriptomics

cnio-bu / beyondcell
spatial-transcriptomics,Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.
Organization: cnio-bu
bioinformatics cancer drugs single-cell spatial-transcriptomics

dana-farber-aios / pathml
spatial-transcriptomics,Tools for computational pathology
Organization: dana-farber-aios
Home Page: https://pathml.org
machine-learning digital-pathology computational-pathology biomedical-image-processing pathology histopathology spatial-transcriptomics image-analysis microscopy fluorescence-microscopy-imaging

dmcable / spacexr
spatial-transcriptomics,Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
User: dmcable
spatial-transcriptomics differential-expression cell-type-identification

euxhenh / cellar
spatial-transcriptomics,Interactive software tool for the assignment of cell types in single-cell studies.
User: euxhenh
Home Page: https://cellar.cmu.hubmapconsortium.org/app/cellar
python gui genomics genomics-visualization clustering singlecell sc-rna-seq sc-atac-seq codex spatial-transcriptomics

flatironinstitute / st_gridnet
spatial-transcriptomics,A Python implementation of the model described in our publication "A convolutional neural network for common-coordinate registration of high-resolution histology images" developed principally for applications to registration of spatial transcriptomics image data.
Organization: flatironinstitute
tissue-registration spatial-transcriptomics neural-networks image-registration visium-st

gao-lab / slat
spatial-transcriptomics,Spatial-Linked Alignment Tool
Organization: gao-lab
Home Page: https://slat.readthedocs.io/en/latest/
bioinformatics single-cell spatial-data spatial-transcriptomics single-cell-analysis deep-learning graph-neural-networks

genecell / cosg
spatial-transcriptomics,Accurate and fast cell marker gene identification with COSG
User: genecell
Home Page: https://cosg.readthedocs.io/en/latest/
single-cell single-cell-rna-seq single-cell-analysis single-cell-atac-seq spatial-transcriptomics

genecell / cosgr
spatial-transcriptomics,Accurate and fast cell marker gene identification with COSG
User: genecell
scrna-seq scatac-seq spatial-transcriptomics marker-genes

gerstung-lab / basiss
spatial-transcriptomics,Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
Organization: gerstung-lab
Home Page: https://doi.org/10.1038/s41586-022-05425-2
cancer-genomics spatial-transcriptomics

guignardlab / napari-sc3d-viewer
spatial-transcriptomics,A plugin to visualise 3D spatial single cell omics
Organization: guignardlab
3d napari napari-plugin python spatial-transcriptomics

gustaveroussy / sopa
spatial-transcriptomics,Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
Organization: gustaveroussy
Home Page: https://gustaveroussy.github.io/sopa/
generalization memory-management pipeline spatial-omics spatial-transcriptomics snakemake spatialdata multiplexed-imaging

haojiawu / cellscopes.jl
spatial-transcriptomics,A Julia package for single cell and spatial data analysis
User: haojiawu
bioinformatics data-viz julia-package single-cell-omics scrna-seq spatial-transcriptomics visium cartana xenium merfish

jefworks-lab / meringue
spatial-transcriptomics,characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
Organization: jefworks-lab
Home Page: https://jef.works/MERINGUE
single-cell spatial-analysis spatial-transcriptomics gene-expression rstats cell-cell-communication

jefworks-lab / mermaid
spatial-transcriptomics,WebGL-based viewer for spatially-resolved transcriptomics data
Organization: jefworks-lab
Home Page: http://jef.works/MERmaid/
webgl data-visualization javascript reactjs single-cell spatial-transcriptomics

jfnavarro / st_pipeline
spatial-transcriptomics,ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
User: jfnavarro
pipeline spatial-transcriptomics visium scrna-seq

jianhuupenn / spagcn
spatial-transcriptomics,SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network
User: jianhuupenn
spatial-transcriptomics graph-convolutional-network spatial-domains spatially-variable-genes

jianhuupenn / tesla
spatial-transcriptomics,Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA
User: jianhuupenn
spatial-transcriptomics tumor-microenvironment super-resolution

jinworks / cellchat
spatial-transcriptomics,R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
Organization: jinworks
cell-cell-communication cell-cell-interaction microenvironment single-cell-analysis spatial-transcriptomics

kharchenkolab / baysor
spatial-transcriptomics,Bayesian Segmentation of Spatial Transcriptomics Data
Organization: kharchenkolab
spatial-transcriptomics segmentation bayesian

kharchenkolab / numbat
spatial-transcriptomics,Haplotype-aware CNV analysis from single-cell RNA-seq
Organization: kharchenkolab
Home Page: https://kharchenkolab.github.io/numbat/
cancer-genomics cnv-detection single-cell phylogeny single-cell-analysis single-cell-rna-seq spatial-transcriptomics lineage-tracing

lhc17 / holonet
spatial-transcriptomics,HoloNet. Reveal the holograph of functional communication events in spatial transcriptomics. Help understand how microenvironments shaping cellular phenotypes
User: lhc17
bioinformatics cell-cell-communication python spatial-transcriptomics

lieberinstitute / humanpilot
spatial-transcriptomics,Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project
Organization: lieberinstitute
Home Page: https://doi.org/10.1038/s41593-020-00787-0
spatial-transcriptomics rstats 10xgenomics visium dlpfc human brain analysis biorxiv

lieberinstitute / spatiallibd
spatial-transcriptomics,Code for the spatialLIBD R/Bioconductor package and shiny app
Organization: lieberinstitute
Home Page: http://LieberInstitute.github.io/spatialLIBD/
rstats shiny spatial-transcriptomics 10xgenomics bioconductor golem visium spatialexperiment spatiallibd

lima1 / sttkit
spatial-transcriptomics,Pipeline for SpatialTranscriptomics and 10X Visium data
User: lima1
visium 10xgenomics spatial-transcriptomics

lmweber / bestpracticesst
spatial-transcriptomics,'Best Practices for Spatial Transcriptomics Analysis with Bioconductor' online book
User: lmweber
Home Page: https://lmweber.org/BestPracticesST/
spatially-resolved-transcriptomics bioconductor spatial-transcriptomics

ma-compbio / spicemix
spatial-transcriptomics,spatial transcriptome, single cell
User: ma-compbio
spatial-transcriptomics single-cell machine-learning

mahmoodlab / hest
spatial-transcriptomics,HEST: Bringing Spatial Transcriptomics and Histopathology together
Organization: mahmoodlab
spatial-transcriptomics computational-pathology histology

nf-core / spatialvi
spatial-transcriptomics,Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Organization: nf-core
Home Page: https://nf-co.re/spatialvi
nf-core nextflow workflow pipeline 10x-genomics 10xgenomics bioinformatics image-processing microscopy rna-seq

omicsml / dance
spatial-transcriptomics,DANCE: a deep learning library and benchmark platform for single-cell analysis
Organization: omicsml
Home Page: https://pydance.readthedocs.io
bioinformatics dance data-science deep-learning graph-neural-networks machine-learning multimodality python single-cell spatial-transcriptomics

pachterlab / voyager
spatial-transcriptomics,From geospatial to spatial -omics
Organization: pachterlab
Home Page: https://pachterlab.github.io/voyager/
bioconductor eda esda exploratory-data-analysis omics r r-package rstats spatial spatial-statistics

rajewsky-lab / openst
spatial-transcriptomics,Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
Organization: rajewsky-lab
Home Page: https://rajewsky-lab.github.io/openst/
bioinformatics omics spatial-transcriptomics transcriptomics

saezlab / decoupler-py
spatial-transcriptomics,Python package to perform enrichment analysis from omics data.
Organization: saezlab
Home Page: https://decoupler-py.readthedocs.io/
python data-science bioinformatics transcriptomics numba single-cell spatial-transcriptomics enrichment enrichment-analysis

saezlab / mistyr
spatial-transcriptomics,Multiview Intercellular SpaTial modeling framework
Organization: saezlab
Home Page: https://saezlab.github.io/mistyR/
multiview intercellular spatial modular biology molecular-biology r spatial-transcriptomics machine-learning bioconductor

scverse / squidpy
spatial-transcriptomics,Spatial Single Cell Analysis in Python
Organization: scverse
Home Page: https://squidpy.readthedocs.io/en/stable/
single-cell-rna-seq single-cell-genomics spatial-transcriptomics spatial-analysis image-analysis data-visualization squidpy

statbiomed / spatialdm
spatial-transcriptomics,Spatial direct messaging detected by bivariate Moran
Organization: statbiomed
Home Page: https://spatialdm.readthedocs.io
cell-cell-communication ligand-receptor-interaction spatial-correlation spatial-transcriptomics

ttgump / spavae
spatial-transcriptomics,Dependency-aware deep generative models for multitasking analysis of spatial genomics data
User: ttgump
deep-learning gaussian-processes spatial-transcriptomics spatial-omics variational-autoencoder pytorch

wanglab-broad / clustermap
spatial-transcriptomics,ClusterMap for multi-scale clustering analysis of spatial gene expression
Organization: wanglab-broad
in-situ-sequencing spatial-transcriptomics single-cell-analysis spatial-omics bioinformatics cell-segmentation transcriptomics

wwxkenmo / enigma
spatial-transcriptomics,A fast and accurate deconvolution algorithm based on regularized matrix completion algorithm (ENIGMA)
User: wwxkenmo
single-cell deconvolution matrix-completion cell-type-deconvolution cell-type-gene-expression-analysis bulk-rna-seq-deconvolution spatial-transcriptomics

yanailab / celseq2
spatial-transcriptomics,Generate the UMI count matrix from CEL-Seq2 sequencing data
Organization: yanailab
Home Page: https://yanailab.github.io/celseq2/
cel-seq2 single-cell-rna-seq bioinformatics-pipeline snakemake umi-count-matrix spatial-transcriptomics

yanglabhkust / stitch3d
spatial-transcriptomics,Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
Organization: yanglabhkust
Home Page: https://stitch3d-tutorial.readthedocs.io/en/latest/index.html#
3d-reconstruction spatial-transcriptomics deep-learning

zijianni / spotclean
spatial-transcriptomics,R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
User: zijianni
rna-seq spatial-transcriptomics

zjufanlab / bulk2space
spatial-transcriptomics,a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles
User: zjufanlab
bulk-sequencing deep-learning scrna-seq spatial-transcriptomics

zjufanlab / scspace
spatial-transcriptomics,an integrative algorithm to distinguish spatially variable cell subclusters by reconstructing cells onto a pseudo space with spatial transcriptome references
User: zjufanlab
scrna-seq spatial-transcriptomics tranfer-learning

zjufanlab / spatalk
spatial-transcriptomics,Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
User: zjufanlab
Home Page: https://github.com/multitalk/awesome-cell-cell-communication
cell-cell-communication cell-cell-interaction knowledge-graph spatial-data-analysis ligand-receptor-interaction graph-network spatially-resolved-transcriptomics spatial-transcriptomics single-cell