scverse/squidpy

Spatial Single Cell Analysis in Python

Language: Python - Size: 10.1 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 489 - Forks: 96

Dana-Farber-AIOS/pathml

Tools for computational pathology

Language: Python - Size: 218 MB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 425 - Forks: 87

jinworks/CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

Language: R - Size: 71.5 MB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 403 - Forks: 68

smorabit/hdWGCNA

High dimensional weighted gene co-expression network analysis

Language: R - Size: 275 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 388 - Forks: 37

dmcable/spacexr

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

Language: HTML - Size: 538 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 363 - Forks: 84

OmicsML/dance

DANCE: a deep learning library and benchmark platform for single-cell analysis

Language: Python - Size: 17.5 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 360 - Forks: 38

aristoteleo/spateo-release

Spatiotemporal modeling of spatial transcriptomics

Language: Python - Size: 34 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 295 - Forks: 39

mahmoodlab/HEST

Integrating histology and spatial transcriptomics - NeurIPS 2024

Language: Python - Size: 36.2 MB - Last synced at: 16 days ago - Pushed at: about 1 month ago - Stars: 278 - Forks: 24

jianhuupenn/SpaGCN

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

Language: Python - Size: 54.1 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 200 - Forks: 59

gustaveroussy/sopa

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

Language: Python - Size: 38.2 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 198 - Forks: 33

saezlab/decoupler-py

Python package to perform enrichment analysis from omics data.

Language: Python - Size: 99.2 MB - Last synced at: about 12 hours ago - Pushed at: about 13 hours ago - Stars: 197 - Forks: 30

kharchenkolab/numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

Language: R - Size: 390 MB - Last synced at: 9 days ago - Pushed at: 20 days ago - Stars: 181 - Forks: 24

kharchenkolab/Baysor

Bayesian Segmentation of Spatial Transcriptomics Data

Language: Julia - Size: 2.12 MB - Last synced at: 23 days ago - Pushed at: 6 months ago - Stars: 174 - Forks: 33

JianYang-Lab/gsMap

Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

Language: Python - Size: 24.7 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 146 - Forks: 14

theMILOlab/SPATA2

A Toolbox for Spatial Transcriptomics Analysis

Language: R - Size: 1.04 GB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 142 - Forks: 20

ZJUFanLab/bulk2space

a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles

Language: Jupyter Notebook - Size: 12.1 MB - Last synced at: 6 months ago - Pushed at: about 2 years ago - Stars: 115 - Forks: 23

rajewsky-lab/openst

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

Language: HTML - Size: 175 MB - Last synced at: 8 days ago - Pushed at: 7 months ago - Stars: 98 - Forks: 17

LieberInstitute/spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

Language: R - Size: 263 MB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 93 - Forks: 20

pachterlab/voyager

From geospatial to spatial -omics

Language: R - Size: 4.32 GB - Last synced at: 26 days ago - Pushed at: 3 months ago - Stars: 92 - Forks: 11

lmweber/OSTA

"Orchestrating Spatial Transcriptomics Analysis with Bioconductor" book

Language: TeX - Size: 65.7 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 89 - Forks: 31

gao-lab/SLAT

Spatial-Linked Alignment Tool

Language: Python - Size: 334 MB - Last synced at: 12 days ago - Pushed at: 6 months ago - Stars: 86 - Forks: 10

alexisvdb/singleCellHaystack

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Language: R - Size: 78.2 MB - Last synced at: 14 days ago - Pushed at: 9 months ago - Stars: 83 - Forks: 9

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: 155 MB - Last synced at: 26 days ago - Pushed at: 3 months ago - Stars: 81 - Forks: 50

LieberInstitute/HumanPilot

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

Language: HTML - Size: 289 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 77 - Forks: 31

ZJUFanLab/SpaTalk

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

Language: R - Size: 9.83 MB - Last synced at: 1 day ago - Pushed at: 5 months ago - Stars: 71 - Forks: 18

JEFworks-Lab/MERINGUE

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Language: R - Size: 89.8 MB - Last synced at: 2 months ago - Pushed at: about 3 years ago - Stars: 69 - Forks: 5

10XGenomics/HumanColonCancer_VisiumHD

Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"

Language: R - Size: 195 MB - Last synced at: 3 days ago - Pushed at: about 1 month ago - Stars: 67 - Forks: 5

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: 7.04 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 64 - Forks: 25

EliHei2/segger_dev

a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).

Language: Python - Size: 5.59 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 64 - Forks: 6

YangLabHKUST/STitch3D

Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices

Language: Python - Size: 11.1 MB - Last synced at: 24 days ago - Pushed at: over 1 year ago - Stars: 64 - Forks: 4

jianhuupenn/TESLA

Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA

Language: Jupyter Notebook - Size: 20.6 MB - Last synced at: 28 days ago - Pushed at: about 1 year ago - Stars: 55 - Forks: 13

saezlab/mistyR

Multiview Intercellular SpaTial modeling framework

Language: R - Size: 126 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 54 - Forks: 11

ma-compbio/SpiceMix

spatial transcriptome, single cell

Language: Jupyter Notebook - Size: 19.1 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 45 - Forks: 7

genecell/COSG

Accurate and fast cell marker gene identification with COSG

Language: Python - Size: 68.8 MB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 44 - Forks: 8

wanglab-broad/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 171 MB - Last synced at: 6 months ago - Pushed at: 11 months ago - Stars: 41 - Forks: 11

cnio-bu/beyondcell

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.

Language: R - Size: 143 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 40 - Forks: 4

HaojiaWu/CellScopes.jl

A Julia package for single cell and spatial data analysis

Language: Julia - Size: 127 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 36 - Forks: 3

single-cell-genetics/XClone

Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.

Language: Python - Size: 4.41 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 36 - Forks: 5

AltschulerWu-Lab/MUSE

MUSE is a deep learning approach characterizing tissue composition through combined analysis of morphologies and transcriptional states for spatially resolved transcriptomics data.

Language: Jupyter Notebook - Size: 153 MB - Last synced at: 14 days ago - Pushed at: about 3 years ago - Stars: 35 - Forks: 8

ratschlab/DeepSpot

DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images

Language: Jupyter Notebook - Size: 37 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 33 - Forks: 5

zijianni/SpotClean

R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data

Language: R - Size: 4.01 MB - Last synced at: 18 days ago - Pushed at: about 1 year ago - Stars: 33 - Forks: 10

genecell/COSGR

Accurate and fast cell marker gene identification with COSG

Language: R - Size: 18.1 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 32 - Forks: 6

euxhenh/cellar

Interactive software tool for the assignment of cell types in single-cell studies.

Language: Python - Size: 51.9 MB - Last synced at: 12 months ago - Pushed at: about 2 years ago - Stars: 31 - Forks: 7

earmingol/scCellFie

scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.

Language: Python - Size: 71.7 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 27 - Forks: 2

StatBiomed/SpatialDM

Spatial direct messaging detected by bivariate Moran

Language: Jupyter Notebook - Size: 51.1 MB - Last synced at: 30 days ago - Pushed at: about 1 month ago - Stars: 26 - Forks: 6

JEFworks-Lab/MERmaid

WebGL-based viewer for spatially-resolved transcriptomics data

Language: JavaScript - Size: 127 MB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 26 - Forks: 5

WWXkenmo/ENIGMA

A fast and accurate deconvolution algorithm based on regularized matrix completion algorithm (ENIGMA)

Language: HTML - Size: 309 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 25 - Forks: 5

flatironinstitute/st_gridnet

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.

Language: Python - Size: 26.8 MB - Last synced at: 2 months ago - Pushed at: over 3 years ago - Stars: 25 - Forks: 4

acycliq/pciSeq

A probabilistic cell typing algorithm for spatial transcriptomics.

Language: Python - Size: 173 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 23 - Forks: 8

ttgump/spaVAE

Dependency-aware deep generative models for multitasking analysis of spatial genomics data

Language: Jupyter Notebook - Size: 22.1 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 23 - Forks: 1

yzf072/spaTrack

An optimal transport-based algorithm for inferring cell trajectories of spatial transcriptomics.

Language: Python - Size: 175 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 22 - Forks: 2

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 at: 3 months ago - Pushed at: 4 months ago - Stars: 22 - Forks: 3

gerstung-lab/BaSISS

Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper

Language: Jupyter Notebook - Size: 30.9 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 22 - Forks: 2

lima1/sttkit

Pipeline for SpatialTranscriptomics and 10X Visium data

Language: R - Size: 648 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 21 - Forks: 7

tare/Splotch

Splotch is a hierarchical generative probabilistic model for analyzing Spatial Transcriptomics (ST) data

Language: Jupyter Notebook - Size: 101 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 21 - Forks: 6

lhc17/HoloNet

HoloNet. Reveal the holograph of functional communication events in spatial transcriptomics. Help understand how microenvironments shaping cellular phenotypes

Language: Python - Size: 6.47 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 21 - Forks: 3

GuignardLab/napari-sc3D-viewer

A plugin to visualise 3D spatial single cell omics

Language: Python - Size: 38.4 MB - Last synced at: 10 months ago - Pushed at: about 1 year ago - Stars: 21 - Forks: 2

sggao/celllens

CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data

Language: Jupyter Notebook - Size: 227 MB - Last synced at: 7 days ago - Pushed at: 14 days ago - Stars: 20 - Forks: 4

yi-zhang/STHD

STHD: probabilistic cell typing of Single spots in whole Transcriptome spatial data with High Definition

Language: Jupyter Notebook - Size: 1.97 MB - Last synced at: 5 days ago - Pushed at: about 1 month ago - Stars: 20 - Forks: 7

yanailab/celseq2

Generate the UMI count matrix from CEL-Seq2 sequencing data

Language: Python - Size: 1.34 MB - Last synced at: about 14 hours ago - Pushed at: over 6 years ago - Stars: 20 - Forks: 13

gao-lab/PASSAGE

Phenotype Associated Spatial Signature Analysis with Graph-based Embedding

Language: Jupyter Notebook - Size: 1.72 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 19 - Forks: 1

ZJUFanLab/scSpace

an integrative algorithm to distinguish spatially variable cell subclusters by reconstructing cells onto a pseudo space with spatial transcriptome references

Language: HTML - Size: 29.6 MB - Last synced at: 12 months ago - Pushed at: about 2 years ago - Stars: 19 - Forks: 3

mehdiborji/nanoranger

simplified cellranger for long-read data

Language: Python - Size: 50.3 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 18 - Forks: 5

HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite

Develop custom oligo design pipelines.

Language: Python - Size: 299 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 17 - Forks: 3

MargoKapustina/XeniumSpatialAnalysis

R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients

Language: R - Size: 374 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 17 - Forks: 2

JEFworks-Lab/SEraster

Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis

Language: R - Size: 43.8 MB - Last synced at: 19 days ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 5

Liao-Xu/SDEvelo

Multivariate stochastic modeling for transcriptional dynamics with cell-specific latent time using SDEvelo

Language: Python - Size: 59.4 MB - Last synced at: 2 days ago - Pushed at: 4 months ago - Stars: 17 - Forks: 2

rockdeme/chrysalis

Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datasets.

Language: Jupyter Notebook - Size: 67.6 MB - Last synced at: 14 days ago - Pushed at: 7 months ago - Stars: 17 - Forks: 0

TheJacksonLaboratory/STQ

Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images

Language: Nextflow - Size: 4.3 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 16 - Forks: 0

jfnavarro/st_analysis

A toolset for analysis and visualisation of Spatial Transcriptomics datasets.

Language: Python - Size: 687 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 16 - Forks: 8

gao-lab/DECIPHER

DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data

Language: Python - Size: 7.41 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 15 - Forks: 0

aristoteleo/spateo-viewer

Web application demonstrating 3D modeling of spatial transcriptomics

Language: Python - Size: 721 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 15 - Forks: 4

xjtu-omics/STMiner

Language: Python - Size: 96.4 MB - Last synced at: about 17 hours ago - Pushed at: about 18 hours ago - Stars: 14 - Forks: 6

AlexsLemonade/scpca-nf

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data

Language: R - Size: 4.17 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 13 - Forks: 2

ratschlab/aestetik

AESTETIK: AutoEncoder for Spatial Transcriptomics Expression with Topology and Image Knowledge

Language: Python - Size: 27.2 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 13 - Forks: 0

ddiez/singleCellHaystack-py

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).

Language: Python - Size: 69 MB - Last synced at: 23 days ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 1

coffee19850519/single_cell_spatial_image

A deep-learning framework for characterizing and visualizing tissue architecture from spatially resolved transcriptomics

Language: Python - Size: 757 MB - Last synced at: 7 months ago - Pushed at: over 2 years ago - Stars: 13 - Forks: 6

SunXQlab/ESICCC

ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methods

Language: R - Size: 23.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 1

lambdamoses/novoSpaRc

Reconstruction of spatial context of gene expression with optimal transport

Language: R - Size: 1.28 MB - Last synced at: 2 months ago - Pushed at: about 6 years ago - Stars: 11 - Forks: 2

sldyns/SpaHDmap

Deep fusion of spatial transcriptomics and histology images for interpretable high-definition embedding mapping

Language: Python - Size: 9.15 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 10 - Forks: 3

JEFworks-Lab/scatterbar

Scatterbar - data visualization for proportional data across many spatially resolved coordinates

Language: R - Size: 13.2 MB - Last synced at: 10 days ago - Pushed at: 3 months ago - Stars: 10 - Forks: 1

stevexniu/spots

Statistical analysis for spatial omics data

Language: R - Size: 38.2 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 10 - Forks: 2

bm2-lab/SpaDo

Multi-slice Spatial Transcriptome Domain Analysis.

Language: R - Size: 2.82 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 9 - Forks: 4

mckellardw/STRS

Suite of analysis tools for spatial total RNA-sequencing

Language: R - Size: 44 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 9 - Forks: 2

hannshu/st_clustering

总结和比较目前发表的处理单细胞空间转录组学(Spatial Transcriptomic)的聚类方法。Conclusion and comparison of the current clustering method for ST data.

Language: Jupyter Notebook - Size: 2.68 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 9 - Forks: 0

ccruizm/GBmap

Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.

Language: Jupyter Notebook - Size: 98.8 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 0

jfnavarro/st_viewer

A GUI tool for easy and smooth visualisation and analysis of Spatial Transcriptomics datasets

Language: C++ - Size: 90.5 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 9 - Forks: 14

hannshu/st_datasets

This repository will continuously collect annotated spatial transcriptomic datasets. 本仓库将持续收集空间转录组数据集

Language: Python - Size: 55.7 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 8 - Forks: 0

doganlab/scmags

Marker Gene Selection Tool For Spatial Transcriptomics

Language: Python - Size: 29.5 MB - Last synced at: 19 days ago - Pushed at: 8 months ago - Stars: 8 - Forks: 1

saezlab/DOT

DOT

Language: R - Size: 27.5 MB - Last synced at: about 2 months ago - Pushed at: 12 months ago - Stars: 8 - Forks: 0

limin321/stmut

Visualizing Somatic Alterations of 10X Spatial Transcriptomics Data

Language: R - Size: 42.2 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 2

jiazhao97/INSPIRE

INSPIRE: interpretable, flexible and spatially-aware integration of multiple spatial transcriptomics datasets from diverse sources

Language: Python - Size: 4.29 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 7 - Forks: 2

bdsc-tds/SPLIT

Profile purification of single-cell spatial transcriptomics data

Language: R - Size: 2.97 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 0

gustaveroussy/CFS

R package using ICA based method for spatial transcriptomics analysis (Visium/Slide-seq/CosMX/MERSCOPE)

Language: R - Size: 22 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 7 - Forks: 2

zhanglabtools/BrainAlign

Code for "Whole brain alignment of spatial transcriptomics between humans and mice with BrainAlign"

Language: Python - Size: 544 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 7 - Forks: 1

LiuLab-Bioelectronics-Harvard/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 300 MB - Last synced at: 6 months ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 2

cellethology/tic

A Unified Framework for Temporal and Causal Inference in Tumor Microenvironments.

Language: Jupyter Notebook - Size: 90.6 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 6 - Forks: 0

YangLabHKUST/MCube

A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies

Language: R - Size: 30.3 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 6 - Forks: 0

ankitbioinfo/nico_tutorial

A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and covariation patterns between interacted cell types.

Language: Jupyter Notebook - Size: 62.5 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 6 - Forks: 3

QI2lab/merfish3d-analysis

GPU accelerated post-processing for 2D or 3D iterative barcoded FISH data.

Language: Python - Size: 3.51 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 6 - Forks: 3