spatial-transcriptomics | Topic | Ecosyste.ms: Repos

Topic: "spatial-transcriptomics"

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: 14 days ago - Pushed at: 14 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: 15 days ago - Pushed at: 16 days ago - Stars: 6 - Forks: 3

TheHumphreysLab/CellScopes.jl Fork of HaojiaWu/CellScopes.jl

A Julia package for single cell and spatial data analysis

Language: Julia - Size: 96.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 1

ratschlab/he2st

Code of the paper "DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images"

Language: Jupyter Notebook - Size: 121 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 1

pedrofale/tumorevo

Simulate the evolution and treatment of tumors and generate bulk, single-cell and spatial data from them.

Language: Jupyter Notebook - Size: 805 KB - Last synced at: about 2 months ago - Pushed at: 5 months ago - Stars: 6 - Forks: 0

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: 6 months ago - Pushed at: 7 months ago - Stars: 6 - Forks: 1

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

NFDI4BIOIMAGE/omero-vitessce

OMERO.web plugin for the Vitessce multimodal data viewer.

Language: Python - Size: 41.3 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 5 - 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: 7 months ago - Pushed at: 7 months ago - Stars: 5 - Forks: 0

diegommcc/SpatialDDLS

Deconvolution of spatial transcriptomics data based on Deep Learning

Language: R - Size: 131 MB - Last synced at: 8 days ago - Pushed at: 8 months ago - Stars: 5 - Forks: 1

qiaochen/tranSpa

Translation-based spatial transcriptomics analysis

Language: Python - Size: 2.24 MB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 5 - 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: 16 days ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 0

pdmoerland/SingleCellNotes

Links to interesting courses, tutorials, papers, software etc. related to single-cell omics data analysis

Size: 114 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 1

secrierlab/EnrichMap

EnrichMap: Spatially-informed enrichment analysis for functional interpretation of spatial transcriptomics.

Language: Python - Size: 89 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 4 - 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: 2 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 2

LieberInstitute/visiumStitched

R package containing functions useful for stitching Visium capture areas. Related to the example human brain data described at http://research.libd.org/visiumStitched_brain/.

Language: R - Size: 26.9 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 4 - Forks: 0

pkosurilab/BellaVista

Python package for interactive visualization of imaging-based spatial transcriptomics

Language: Python - Size: 96.5 MB - Last synced at: 21 days ago - Pushed at: 6 months ago - Stars: 4 - Forks: 1

az7jh2/SDePER

Spatial Deconvolution method with Platform Effect Removal

Language: Python - Size: 1.41 MB - Last synced at: 18 days ago - Pushed at: 8 months ago - Stars: 4 - 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: 3 months ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0

ZJUFanLab/SpaTrio

Language: Python - Size: 74.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

lmassier/hWAT_singlecell

meta-analysis of new and published human WAT single cell data

Language: R - Size: 256 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 0

gurbaaz27/cs690a-clustering-spatial-transcriptomics-data

Course Assignment on Clustering of Spatial Transcriptomics Data

Language: Jupyter Notebook - Size: 62.2 MB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 0

yintz/SPACEmapX

SPACEmapX

Language: R - Size: 12.5 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 3 - Forks: 0

HuifangZJU/Vispro

Vispro improves imaging analysis for Visium spatial1 transcriptomics

Language: Python - Size: 36.6 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 3 - Forks: 0

Liuy12/STITCH

Spatial and single-cell Transcriptomics Integration Tool for CHaracterization (STITCH)

Language: R - Size: 3.35 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0

YukiZH/SCOIGET

A Tool for Predicting Spatial Tumor Evolution Pattern by Inferring Spatial Copy Number Variation Distributions

Language: Jupyter Notebook - Size: 30.8 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 3 - 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: 11 months ago - Pushed at: 11 months ago - Stars: 3 - Forks: 0

TingruiZh/spatial_transcriptomics_ml_frameworks-SUMMARY

This repository summarizes recent machine learning (ML) frameworks applied in spatial transcriptomics data analysis. These methods focus on discovering spatial domains, cell types, and embedding representations from high-dimensional single-cell gene expression data.

Language: Jupyter Notebook - Size: 457 KB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 2 - Forks: 0

jr-leary7/bayesVG

Identify variable genes in scRNA-seq and spatial transcriptomics data using Bayesian inference

Language: R - Size: 26.1 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 2 - Forks: 0

KrishnaswamyLab/hypergraph-wavelets

Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics

Language: Python - Size: 106 KB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 2 - Forks: 1

Qingyueee/DECLUST

A cluster-based cell-type deconvolution of spatial transcriptomic data

Language: Jupyter Notebook - Size: 18.1 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

phipsonlab/jazzPanda

A hybrid approach to find spatially relevant marker genes in image based spatial transcriptomics data

Language: R - Size: 24.9 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 1

christinehou11/BatchSVG

Identification of biased features from SVGs in spatial transcriptomics data

Language: R - Size: 15.5 MB - Last synced at: 26 days ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

jaychowcl/benchdeconv

A benchmarking pipeline for spatial deconvolution methods!

Language: R - Size: 2.13 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 1

ThomasGust/Elastic-ST

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: 24 days ago - Pushed at: 5 months ago - Stars: 2 - 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

seqscope/NovaScope

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

Language: Python - Size: 52.9 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 2 - 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

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

acycliq/visage

A 2D spatial trancriptomics web viewer

Language: JavaScript - Size: 173 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 1

sheffield-bioinformatics-core/spatial_transcriptomics_tutorial

A bare bones tutorial on how to analyse spatial transcriptomics data from raw sequencing reads to visualising spatially distinct features

Language: HTML - Size: 150 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

alexzli/UROP

Unsupervised cell type identification for spatial transcriptomics

Language: R - Size: 22.2 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

estfernan/boost

A collection of novel and standard statistical techniques for detecting spatially variable (SV) genes in spatial transcriptomics (ST) data.

Language: R - Size: 4.72 MB - Last synced at: 13 days ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 1

vertesy/C.elegans.Spatial.Transcriptomics

Analysis scripts for the Ebbing et manuscript: "Spatially-resolved transcriptomics in C. elegans identifies sex-specific differences in gene expression patterns"

Language: R - Size: 54.7 KB - Last synced at: over 2 years ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 1

ladislav-hovan/stoat

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

Language: Python - Size: 150 KB - Last synced at: about 18 hours ago - Pushed at: about 19 hours ago - Stars: 1 - Forks: 0

TGAC/SingleCellSchemas

For resources related to the EI Cellgen ISP, including metadata mappings and schemas for Single Cell Genomics and Spatial Transcriptomics experiments.

Language: CSS - Size: 11 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 1 - Forks: 0

shiquan/Yano

An R package to perform Spatial dissimilarity analysis in single cells

Language: C - Size: 10.1 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 1 - Forks: 0

KalinNonchev/azimuthpy

Annotate your single-cell data using Azimuth in python.

Language: Jupyter Notebook - Size: 26.4 KB - Last synced at: 21 days ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

lyotvincent/CUCA

CUCA: Predicting fine-grained cell types from histology images through cross-modal learning in spatial transcriptomics

Language: Python - Size: 1.16 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

PSSUN/STMiner2 Fork of xjtu-omics/STMiner

Language: Python - Size: 96.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

wanglab-broad/FuseMap

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

Language: Jupyter Notebook - Size: 70.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

rouni001/Differential-Velocity

Python methods for computing Differential Velocity

Language: Python - Size: 12.7 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

secrierlab/G0-breast-cancer-atlas

G0 breast cancer atlas

Language: R - Size: 320 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - 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: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

skimlab/spatialCCC

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

Language: HTML - Size: 74 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 1

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: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

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: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 2

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: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 3

srivarra/anatomize

Xarray powered Image analysis toolkit.

Language: Python - Size: 111 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - 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

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

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

Lu18835713910/Museum-of-Spatial-Transcriptomics--

本仓主要为将"Museum of spatial transcriptomics"中的线上数据库： https://github.com/pachterlab/LP_2021 中文字资源整理为中文版本（文字资源内容截止至2024年2月15日）后续将仿照原链接中工作流整理为线上及时更新的中文数据文档；本仓已与作者本人沟通过，征得了本人的同意，且作者也表示后续将在2025年推出第二版，后期我也将持续更新；打工人业余时间整理，更新不及时还请见谅。

Size: 11 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

OlivierRaineteauSBRI/scRNASeq

Repo linked to our recent publication in Science Advances

Language: HTML - Size: 5.66 GB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

Lordsupreme/4t1-tnbc-spatial-scrna

This repository contains tools for analyzing spatial single-cell RNA sequencing data in triple-negative breast cancer (TNBC). Explore the integration of spatial information with transcriptomic profiles to uncover insights into tumor microenvironments. 🐙🌟

Language: Python - Size: 2.93 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

Rakgnar/Global-AI-Kaggle-Hackathon-2025-Elucidata

This repository offers a deep learning solution for predicting spatial cell-type compositions from histology images, achieving a top 204 rank in the Global AI Kaggle Hackathon 2025. Explore the code and methodologies used to extract and analyze image data effectively. 🐱💻📊

Language: Python - Size: 804 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

smcclatchy/spatial-transcriptomics

Language: JavaScript - Size: 1.45 GB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 3

sviatkh/spatial-transcriptomics-project

Capstone project was performed during the course "Introduction to R and RNA sequencing". https://sviatkh.github.io/spatial-transcriptomics-project/

Language: Jupyter Notebook - Size: 72.5 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 0 - Forks: 0

hannshu/stSCI

Joint analysis single-cell and spatial transcriptomics data with stSCI

Language: Python - Size: 9.22 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 0 - Forks: 0

Jingwe-Zhao/SpotOnco

A universal tool for rapid identification of cancer foci and tumor boundaries in spatial transcriptome

Language: R - Size: 69.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

MengqianHuang/MIXER Fork of ToryDeng/LEGEND

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

Language: Python - Size: 142 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0