GitHub topics: spatial-transcriptomics

Repositories

christinehou11/BatchSVG

Identification of biased features from SVGs in spatial transcriptomics data

Language: R - Size: 15.5 MB - Last synced at: 24 days ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

0x644BE25/Syrah_manuscript

Code to generate figures for Syrah manuscript

Language: R - Size: 73.2 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

PSSUN/STMiner2 Fork of xjtu-omics/STMiner

Language: Python - Size: 96.5 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

smorabit/hdWGCNA

High dimensional weighted gene co-expression network analysis

Language: R - Size: 275 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 388 - Forks: 37

yzf072/spaTrack

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

Language: Python - Size: 175 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 22 - Forks: 2

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: 4 months ago - Pushed at: about 3 years ago - Stars: 69 - Forks: 5

A python data science library to build and analyze biological networks from spatial transcriptomics data. Allows inclusion of spatial information into the networks, going a step beyond graphs derived from scRNA-seq techniques.

Language: Python - Size: 46.7 MB - Last synced at: 16 days ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0

PascaDiMagliano-Lab/Gift-of-Life-Public-Repository

This is repo for the code used in (Carpenter, Elhossiny, Kadiyala et al, Cancer Discovery, 2023) paper from the Pasca lab

Language: R - Size: 5.62 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 2

wanglab-broad/FuseMap

FuseMap: Integrate spatial transcripomics with universal gene, cell, and tissue embeddings.

Language: Jupyter Notebook - Size: 70.1 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

rouni001/Differential-Velocity

Python methods for computing Differential Velocity

Language: Python - Size: 12.7 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

ladislav-hovan/stoat

Python package to generate spatially resolved gene regulatory networks from spatial transcriptomics data.

Language: Python - Size: 177 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 1 - Forks: 0

gao-lab/PASSAGE

Phenotype Associated Spatial Signature Analysis with Graph-based Embedding

Language: Jupyter Notebook - Size: 1.72 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 19 - Forks: 1

jaychowcl/benchdeconv

A benchmarking pipeline for spatial deconvolution methods!

Language: R - Size: 2.13 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 1

zhou-ran/SCAR

Spatially-resolved Chimeric AnalyzeR

Language: R - Size: 104 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 0 - 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: 5 months ago - Pushed at: 5 months ago - Stars: 16 - Forks: 0

secrierlab/G0-breast-cancer-atlas

G0 breast cancer atlas

Language: R - Size: 320 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 1

NFDI4BIOIMAGE/omero-vitessce

OMERO.web plugin for the Vitessce multimodal data viewer.

Language: Python - Size: 41.3 MB - Last synced at: 2 months ago - Pushed at: 5 months ago - Stars: 5 - Forks: 0

LieberInstitute/HumanPilot

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

Language: HTML - Size: 289 MB - Last synced at: 4 months ago - Pushed at: about 1 year ago - Stars: 77 - Forks: 31

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: 4 days ago - Pushed at: 6 months ago - Stars: 17 - Forks: 3

diegommcc/SpatialDDLS

Deconvolution of spatial transcriptomics data based on Deep Learning

Language: R - Size: 131 MB - Last synced at: 7 days ago - Pushed at: 9 months ago - Stars: 5 - Forks: 1

digitalcytometry/spatialecotyper

Spatial EcoTyper is a machine learning framework for systematic identification of spatially distinct multicellular communities from single-cell spatial transcriptomics data.

Language: R - Size: 30.7 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

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: 7 months ago - Pushed at: 7 months ago - Stars: 8 - Forks: 0

bm2-lab/SpaDo

Multi-slice Spatial Transcriptome Domain Analysis.

Language: R - Size: 2.82 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 9 - Forks: 4

skimlab/spatialCCC

Investigate cell-cell signaling, by analyzing ligand-receptor interactions in spatial transcriptomic data

Language: HTML - Size: 74 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 1

aristoteleo/spateo-viewer

Web application demonstrating 3D modeling of spatial transcriptomics

Language: Python - Size: 721 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 15 - Forks: 4

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: 7 months ago - Pushed at: over 2 years ago - Stars: 115 - Forks: 23

YifeiSheng/Cytocraft

The Cytocraft package provides 3D reconstruction of spatial configuration of transcription centers

Language: Jupyter Notebook - Size: 130 MB - Last synced at: about 22 hours ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

christinehou11/humanHippocampus2024

Access to spatial HPC project data

Language: R - Size: 1.64 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 1

jianhuupenn/MorphLink

MorphLink: Bridging Cellular Morphological Behaviors and Molecular Dynamics in Multi-modal Spatial Omics

Language: Jupyter Notebook - Size: 59.1 MB - Last synced at: 7 months ago - Pushed at: 8 months ago - Stars: 6 - Forks: 1

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 at: 4 months ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0

qiaochen/tranSpa

Translation-based spatial transcriptomics analysis

Language: Python - Size: 2.24 MB - Last synced at: 6 days ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 0

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: 8 months ago - Pushed at: almost 2 years ago - Stars: 200 - Forks: 59

Layla-R/KTx-fibrosis-study

Repository containing R scripts required to replicate the KTx rejection spatial analysis part of this study.

Language: R - Size: 200 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

Teichlab/thymus_spatial_atlas

general repo that holds all analysis and figures for the thymus spatial atlas by Yayon, Kedlian, Boehme, Radtke and many more!

Language: Jupyter Notebook - Size: 395 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 5 - Forks: 0

C0nc/TAICHI

A Python package for the Scalable and accurate identification condition-relevant niches from spatial -omics data.

Language: Jupyter Notebook - Size: 9.43 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 2 - Forks: 0

LitingKu/SpaCCI

SpaCCI: Spatially Aware Cell-Cell Interaction Analysis

Language: R - Size: 15.7 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

swainasish/ScInfeR

graph-based cell type annotation toolkit for single-cell RNA-seq, ATAC-seq, and spatial omics

Language: R - Size: 31.4 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

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: 3 months ago - Pushed at: 11 months ago - Stars: 21 - Forks: 3

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: 9 months ago - Pushed at: almost 3 years ago - Stars: 13 - Forks: 6

yanailab/celseq2

Generate the UMI count matrix from CEL-Seq2 sequencing data

Language: Python - Size: 1.34 MB - Last synced at: 2 days ago - Pushed at: almost 7 years ago - Stars: 20 - Forks: 13

saezlab/DOT

DOT

Language: R - Size: 27.5 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 0

wanglab-broad/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 171 MB - Last synced at: 8 months ago - Pushed at: 12 months ago - Stars: 41 - Forks: 11

sldyns/DeepFuseNMF

Interpretable high-resolution dimension reduction of spatial transcriptomics data

Language: Python - Size: 10.1 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 1

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: 10 months ago - Pushed at: 10 months ago - Stars: 40 - Forks: 4

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: 10 months ago - Pushed at: 10 months ago - Stars: 7 - Forks: 2

az7jh2/SDePER_Analysis

This Github repository holds data, Notebooks and results of running SDePER on both Simulated and Real datasets, and Notebooks for figure panels in manuscript, as well as the codes for running other cell type deconvolution methods.

Language: HTML - Size: 224 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - 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: 10 months ago - Pushed at: 10 months ago - Stars: 7 - Forks: 1

mckellardw/DWM_utils

Tools, wrappers, utilities, and resources for handling single-cell and spatial transcriptomics data

Language: Python - Size: 60.1 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 3

srivarra/anatomize

Xarray powered Image analysis toolkit.

Language: Python - Size: 111 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

Jianglab1/SC_DRG-bulk_single_spatial

Codes for integrating spatial transcriptomics and single-nucleus RNA-Sequencing uncovering neuropathic pain-associated molecular pathological characteristics in the mouse spinal cord.

Language: R - Size: 28.3 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

seqscope/NovaScope

The pipeline to process Novaseq dataset, from fastq to nge.

Language: Python - Size: 52.9 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0

feiyoung/DR.SC

DR.SC: Joint dimension reduction and spatial clustering for single-cell/spatial transcriptomics data

Language: C++ - Size: 42.9 MB - Last synced at: 13 days ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 0

HKU-BAL/CellContrast

CellContrast: Reconstructing Spatial Relationships in Single-Cell RNA Sequencing Data via Deep Contrastive Learning

Language: Jupyter Notebook - Size: 1.01 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 3 - Forks: 0

antosalerno/TEPA_code_v2.0

Analysing single-cell and DSP data to test the effect of copper chelation with TEPA in Neuroblastoma mice

Language: R - Size: 114 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

antosalerno/TEPA_code

Analysing single-cell and DSP data to test the effect of copper chelation with TEPA in Neuroblastoma mice

Language: R - Size: 650 KB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

ttgump/spaVAE

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

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

chevrierlab/ArraySeq

Analysis of Array-seq ST Datasets

Language: Python - Size: 7.47 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

namini94/MUSTANG

MUSTANG: reference-free MUlti-sample Spatial Transcriptomics data ANalysis with cross-sample transcriptional similarity Guidance

Language: Python - Size: 3.36 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

ZJUFanLab/scCube

an SRT simulator for simulating multiple spatial variability in spatial resolved transcriptomics and generating unbiased simulated SRT data

Language: Jupyter Notebook - Size: 71 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 0

ratschlab/st-rep

Code of the paper "Representation learning for multi-modal spatially resolved transcriptomics data"

Language: Jupyter Notebook - Size: 101 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

phipsonlab/spaceMarker

Language: R - Size: 18.1 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

JEFworks-Lab/MERmaid

WebGL-based viewer for spatially-resolved transcriptomics data

Language: JavaScript - Size: 127 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 26 - Forks: 5

TauConsortium/adad-nucseq-psen1

Repository containing the computational code for Single Nucleus RNA Sequencing Demonstrates an Autosomal Dominant Alzheimer’s Disease Profile and Possible Mechanism of Disease Protection manuscript by Almeida et al.

Language: R - Size: 146 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

euxhenh/cellar

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

Language: Python - Size: 51.9 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 31 - Forks: 7

cb11711211/sc_st_attention_integration

The model and algorithm about how to implement the integration of single-cell RNA-seq and spatial transcriptomics through attention mechanism

Language: Jupyter Notebook - Size: 86.1 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

ToryDeng/LEGEND

LEGEND: An integrative algorithm for identifying co-expressed and cofunctional genes in multimodal transcriptomic sequencing data

Language: Python - Size: 135 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

hannshu/stCluster

Accurate spatial domain deciphering for spatially resolved transcriptomics with stCluster

Language: Python - Size: 27.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 1

LSeu-Open/Enhanced-BioResearch

A curated list of repositories featuring articles, software, tools, pipelines, plugins, and more for biology research needs.

Size: 201 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

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: 1 day ago - Pushed at: over 3 years ago - Stars: 25 - Forks: 4