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Search results for spatial transcriptomics
spatial-transcriptomics
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60 search results found
Squidpy
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362
Spatial Single Cell Analysis in Python
Pathml
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341
Tools for computational pathology
Dance
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284
DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis
Spacexr
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225
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
Spagcn
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157
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network
Spateo Release
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135
Spatiotemporal modeling of spatial transcriptomics
Baysor
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113
Bayesian Segmentation of Spatial Transcriptomics Data
Decoupler Py
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112
Python package to perform enrichment analysis from omics data.
Cellchat
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76
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
Singlecellhaystack
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68
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
Bulk2space
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68
a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles
Spatiallibd
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53
Code for the spatialLIBD R/Bioconductor package and shiny app
Slat
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52
Spatial-Linked Alignment Tool
Voyager
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49
From geospatial to spatial -omics
Spicemix
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41
spatial transcriptome, single cell
Spatalk
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37
Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
Humanpilot
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34
Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project
Spatialtranscriptomics
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34
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Tesla
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33
Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA
Meringue
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33
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
Cellar
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30
Interactive software tool for the assignment of cell types in single-cell studies.
Stitch3d
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27
Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
Mistyr
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27
Multiview Intercellular SpaTial modeling framework
Mermaid
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26
WebGL-based viewer for spatially-resolved transcriptomics data
Sopa
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25
Technology-invariant pipeline for spatial-omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
Cosg
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22
Accurate and fast cell marker gene identification with COSG
Enigma
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22
A fast and accurate deconvolution algorithm based on regularized matrix completion algorithm (ENIGMA)
Cosgr
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20
Accurate and fast cell marker gene identification with COSG
Bestpracticesst
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19
'Best Practices for Spatial Transcriptomics Analysis with Bioconductor' online book
Clustermap
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18
ClusterMap for multi-scale clustering analysis of spatial gene expression
Pciseq
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17
A probabilistic cell typing algorithm for spatial transcriptomics.
Splotch
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17
Splotch is a hierarchical generative probabilistic model for analyzing Spatial Transcriptomics (ST) data
Sttkit
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16
Pipeline for SpatialTranscriptomics and 10X Visium data
Spatialdm
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16
Spatial direct messaging detected by bivariate Moran
Napari Sc3d Viewer
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16
A plugin to visualise 3D spatial single cell omics
Holonet
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14
HoloNet. Reveal the holograph of functional communication events in spatial transcriptomics. Help understand how microenvironments shaping cellular phenotypes
Chrysalis
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13
Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datasets.
Oligo Designer Toolsuite
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12
Develop custom oligo design pipelines.
St_gridnet
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12
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.
Esiccc
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11
ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methods
Spotclean
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11
R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
Scpca Nf
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11
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
Basiss
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11
Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
Spateo Viewer
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10
Web application demonstrating 3D modeling of spatial transcriptomics
Scspace
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10
an integrative algorithm to distinguish spatially variable cell subclusters by reconstructing cells onto a pseudo space with spatial transcriptome references
Cellscopes.jl
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9
A Julia package for single cell and spatial data analysis
Muse
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9
MUSE is a deep learning approach characterizing tissue composition through combined analysis of morphologies and transcriptional states for spatially resolved transcriptomics data.
Strs
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9
Suite of analysis tools for spatial total RNA-sequencing
Singlecellhaystack Py
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8
Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).
St_analysis
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8
A toolset for analysis and visualisation of Spatial Transcriptomics datasets.
Single_cell_spatial_image
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8
A deep-learning framework for characterizing and visualizing tissue architecture from spatially resolved transcriptomics
Spatialdlpfc
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7
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
Stq
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7
Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
St_pipeline
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6
ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
Novosparc
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6
Reconstruction of spatial context of gene expression with optimal transport
Dr.sc
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5
DR.SC: Joint dimension reduction and spatial clustering for single-cell/spatial transcriptomics data
Spatrio
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5
Spavae
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5
Dependency-aware deep generative models for multitasking analysis of spatial genomics data
Celseq2
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5
Generate the UMI count matrix from CEL-Seq2 sequencing data
Singlecellnotes
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5
Links to interesting courses, tutorials, papers, software etc. related to single-cell omics data analysis
Related Searches
Python Spatial Transcriptomics (23)
Single Cell Spatial Transcriptomics (16)
Jupyter Notebook Spatial Transcriptomics (16)
Bioinformatics Spatial Transcriptomics (15)
R Spatial Transcriptomics (15)
Deep Learning Spatial Transcriptomics (11)
Spatial Transcriptomics Visium (6)
Single Cell Rna Seq Spatial Transcriptomics (5)
Machine Learning Spatial Transcriptomics (5)
Rstats Spatial Transcriptomics (5)
1-60 of 60 search results
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