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Spatial Single Cell Analysis in Python
Created
2020-08-21
627 commits to main branch, last one 25 days ago
Tools for computational pathology
Created
2019-07-31
1,011 commits to master branch, last one 2 months ago
DANCE: a deep learning library and benchmark platform for single-cell analysis
Created
2022-06-07
785 commits to main branch, last one 12 days ago
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
Created
2020-02-06
331 commits to master branch, last one 4 months ago
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
Created
2023-11-05
105 commits to main branch, last one 9 days ago
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network
Created
2020-10-21
290 commits to master branch, last one 9 months ago
Haplotype-aware CNV analysis from single-cell RNA-seq
Created
2021-05-25
943 commits to main branch, last one 24 days ago
Spatiotemporal modeling of spatial transcriptomics
Created
2021-02-22
1,635 commits to main branch, last one 2 days ago
Python package to perform enrichment analysis from omics data.
Created
2021-11-16
584 commits to main branch, last one 8 days ago
Bayesian Segmentation of Spatial Transcriptomics Data
Created
2019-01-23
848 commits to master branch, last one 11 days ago
a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles
Created
2021-12-31
99 commits to main branch, last one about a year ago
Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
Created
2023-09-04
767 commits to master branch, last one 17 days ago
Code for the spatialLIBD R/Bioconductor package and shiny app
Created
2019-12-04
631 commits to devel branch, last one about a month ago
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
Created
2019-02-13
446 commits to master branch, last one 5 months ago
HEST: Bringing Spatial Transcriptomics and Histopathology together
Created
2024-03-04
7 commits to main branch, last one 3 days ago
Spatial-Linked Alignment Tool
Created
2022-10-25
24 commits to main branch, last one 21 days ago
Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project
Created
2019-12-04
214 commits to master branch, last one about a month ago
From geospatial to spatial -omics
Created
2020-07-22
468 commits to main branch, last one 24 days ago
spatial transcriptome, single cell
Created
2019-11-07
79 commits to master branch, last one about a year ago
ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
Created
2016-07-10
846 commits to master branch, last one 3 years ago
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
Created
2018-04-26
184 commits to master branch, last one 2 years ago
Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
Created
2023-09-08
451 commits to main branch, last one 11 days ago
Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
Created
2022-03-29
166 commits to main branch, last one 15 days ago
Accurate and fast cell marker gene identification with COSG
Created
2021-06-15
18 commits to main branch, last one about a year ago
Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
Created
2022-11-17
69 commits to main branch, last one 7 months ago
Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.
Created
2022-08-12
23 commits to main branch, last one about a year ago
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Created
2022-02-23
611 commits to dev branch, last one about a month ago
ClusterMap for multi-scale clustering analysis of spatial gene expression
Created
2021-09-29
74 commits to main branch, last one about a month ago
Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA
Created
2021-11-14
85 commits to main branch, last one 3 months ago
Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.
Created
2022-05-30
166 commits to master branch, last one 4 months ago