scverse/decoupler

Python package to perform enrichment analysis from omics data.

Language: Python - Size: 112 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 215 - Forks: 32

hannshu/stSCI

Joint analysis single-cell and spatial transcriptomics data with stSCI

Language: Python - Size: 9.23 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

lmweber/OSTA

"Orchestrating Spatial Transcriptomics Analysis with Bioconductor" book

Language: TeX - Size: 66.4 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 88 - Forks: 34

mckellardw/slide_snake

Snakemake pipeline for the preprocessing, alignment, QC, and quantification of spatial transcriptomics data - both short-read and long-read

Language: Python - Size: 62.9 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 8 - Forks: 6

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: 42 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 210 - Forks: 34

OmicsML/dance

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

Language: Python - Size: 17.7 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 368 - Forks: 38

scverse/squidpy

Spatial Single Cell Analysis in Python

Language: Python - Size: 10.1 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 499 - Forks: 97

ratschlab/DeepSpot

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

Language: Jupyter Notebook - Size: 37 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 49 - Forks: 8

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: about 15 hours ago - Pushed at: about 2 months ago - Stars: 87 - Forks: 7

KrishnaswamyLab/hypergraph-wavelets

Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics

Language: Python - Size: 1.92 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 4 - Forks: 1

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: 11 days ago - Pushed at: 11 days ago - Stars: 381 - Forks: 85

QI2lab/merfish3d-analysis

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

Language: Python - Size: 3.63 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 6 - Forks: 3

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: 9 days ago - Pushed at: almost 2 years ago - Stars: 230 - Forks: 64

kharchenkolab/numbat

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

Language: R - Size: 390 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 186 - Forks: 25

Layla-R/KTx-fibrosis-study

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

Language: R - Size: 82 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

sldyns/SpaHDmap

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

Language: Python - Size: 25 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 10 - Forks: 4

shiquan/Yano

An R package to perform Spatial dissimilarity analysis in single cells

Language: C - Size: 10.1 MB - Last synced at: 13 days ago - Pushed at: 14 days ago - Stars: 1 - Forks: 0

nf-core/sopa

Nextflow version of Sopa - spatial omics pipeline and analysis

Language: Nextflow - Size: 437 KB - Last synced at: 13 days ago - Pushed at: 14 days ago - Stars: 1 - Forks: 1

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: 13 days ago - Pushed at: 14 days ago - Stars: 159 - Forks: 15

AlexsLemonade/scpca-nf

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

Language: R - Size: 4.43 MB - Last synced at: about 11 hours ago - Pushed at: about 11 hours ago - Stars: 14 - Forks: 2

jdutel42/MpBC_project

Spatial transcriptomics of MpBC. This project analyzes spatial transcriptomics data from 15 metaplastic breast carcinoma (MpBC) samples using 10x Genomics Visium. It aims to explore tumor heterogeneity and transdifferentiation, leveraging expert-labeled cell types to identify spatial clusters and biomarkers.

Language: Jupyter Notebook - Size: 650 MB - Last synced at: 14 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

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: 14 days ago - Pushed at: 15 days ago - Stars: 29 - Forks: 2

cellethology/tic

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

Language: Jupyter Notebook - Size: 105 MB - Last synced at: 14 days ago - Pushed at: 15 days ago - Stars: 7 - Forks: 0

alexisvdb/singleCellHaystack

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

Language: R - Size: 78.2 MB - Last synced at: 3 days ago - Pushed at: 11 months ago - Stars: 84 - Forks: 9

secrierlab/EnrichMap

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

Language: Python - Size: 89 MB - Last synced at: 16 days ago - Pushed at: about 2 months ago - Stars: 6 - Forks: 1

Lotfollahi-lab/mintflow

Generation of disentangled microenvironment-induced and intrinsic gene expression vectors from spatial transcriptomics data

Language: Python - Size: 18.7 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 2 - 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: 60.3 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 7 - Forks: 3

gao-lab/DECIPHER

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

Language: Python - Size: 12.4 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 15 - Forks: 0

YangLabHKUST/MCube

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

Language: R - Size: 121 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 7 - Forks: 0

sggao/celllens

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

Language: Jupyter Notebook - Size: 229 MB - Last synced at: 11 days ago - Pushed at: about 2 months ago - Stars: 26 - Forks: 6

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: 24 days ago - Pushed at: 24 days ago - Stars: 0 - Forks: 0

xjtu-omics/STMiner

Language: Python - Size: 110 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 15 - Forks: 7

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: 25 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 0

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: 7.09 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 65 - Forks: 25

Dana-Farber-AIOS/pathml

Tools for computational pathology

Language: Python - Size: 218 MB - Last synced at: 24 days ago - Pushed at: 26 days ago - Stars: 429 - Forks: 87

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: 11 days ago - Pushed at: 5 months ago - Stars: 85 - Forks: 51

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: 1 day ago - Pushed at: 3 months ago - Stars: 18 - Forks: 5

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: 28 days ago - Pushed at: 28 days ago - Stars: 5 - Forks: 0

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: 11 days ago - Pushed at: over 1 year ago - Stars: 66 - Forks: 4

aristoteleo/spateo-release

Spatiotemporal modeling of spatial transcriptomics

Language: Python - Size: 33.1 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 303 - Forks: 40

MicTott/SpotSweeper

Spatially-aware quality control for spatial transcriptomics

Language: R - Size: 36.9 MB - Last synced at: 4 days ago - Pushed at: 7 months ago - Stars: 9 - Forks: 1

single-cell-genetics/XClone

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

Language: Python - Size: 4.44 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 36 - Forks: 5

smcclatchy/spatial-transcriptomics

Language: JavaScript - Size: 1.49 GB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 3

genecell/COSG

Accurate and fast cell marker gene identification with COSG

Language: Python - Size: 68.8 MB - Last synced at: 27 days ago - Pushed at: 4 months ago - Stars: 45 - Forks: 8

gao-lab/SLAT

Spatial-Linked Alignment Tool

Language: Python - Size: 334 MB - Last synced at: 25 days ago - Pushed at: 7 months ago - Stars: 87 - Forks: 10

HaojiaWu/CellScopes.jl

A Julia package for single cell and spatial data analysis

Language: Julia - Size: 127 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 38 - Forks: 3

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

A Julia package for single cell and spatial data analysis

Language: Julia - Size: 98.1 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 8 - Forks: 1

bdsc-tds/SPLIT

Profile purification of single-cell spatial transcriptomics data

Language: R - Size: 3.01 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 14 - Forks: 0

HuifangZJU/Vispro

Vispro improves imaging analysis for Visium spatial1 transcriptomics

Language: Python - Size: 36.6 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 1

poncey/STForte

Enhanced spatially resolved transcriptomics analysis by matching between expression profiles and spatial topology.

Language: Jupyter Notebook - Size: 22.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 1

phipsonlab/jazzPanda

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

Language: R - Size: 25 MB - Last synced at: about 1 month ago - Pushed at: about 1 month 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: 17 days ago - Pushed at: 3 months ago - Stars: 3 - Forks: 1

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: 26 days ago - Pushed at: 8 months ago - Stars: 101 - Forks: 18

pkosurilab/BellaVista

Python package for interactive visualization of imaging-based spatial transcriptomics

Language: Python - Size: 96.5 MB - Last synced at: about 6 hours ago - Pushed at: 7 months ago - Stars: 5 - Forks: 1

GuignardLab/napari-sc3D-viewer

A plugin to visualise 3D spatial single cell omics

Language: Python - Size: 38.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 22 - Forks: 2

HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite

Develop custom oligo design pipelines.

Language: Python - Size: 301 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 18 - Forks: 4

SciComp8/NGSOmics_Programming

Computational biology/bioinformatics workflows, codes, tech & concept notes on NGS data

Language: HTML - Size: 8.32 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - 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: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

StatBiomed/SpatialDM

Spatial direct messaging detected by bivariate Moran

Language: Jupyter Notebook - Size: 50.4 MB - Last synced at: 15 days ago - Pushed at: 18 days ago - Stars: 27 - Forks: 6

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: 25 days ago - Pushed at: 3 months ago - Stars: 22 - Forks: 7

scverse/202504_workshop_GSCN 📦

Language: Jupyter Notebook - Size: 190 MB - Last synced at: 23 days ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0

pachterlab/voyager

From geospatial to spatial -omics

Language: R - Size: 4.32 GB - Last synced at: 10 days ago - Pushed at: 5 months ago - Stars: 95 - Forks: 12

acycliq/pciSeq

A probabilistic cell typing algorithm for spatial transcriptomics.

Language: Python - Size: 173 MB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 24 - Forks: 8

ratschlab/aestetik

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

Language: Python - Size: 27.2 MB - Last synced at: 3 days ago - Pushed at: about 2 months ago - Stars: 14 - Forks: 2

JEFworks-Lab/scatterbar

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

Language: R - Size: 13.2 MB - Last synced at: 27 days ago - Pushed at: 5 months ago - Stars: 11 - Forks: 1

xinglab-ai/ccsf

Leveraging cell-cell similarity for high-performance spatial and temporal cellular mappings from gene expression data (Cell Patterns, 2023)

Language: Python - Size: 6.65 MB - Last synced at: 27 days ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 2

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: 2 days ago - Pushed at: about 1 year ago - Stars: 32 - Forks: 10

jianhuupenn/TESLA

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

Language: Jupyter Notebook - Size: 20.6 MB - Last synced at: 6 days ago - Pushed at: over 1 year ago - Stars: 57 - Forks: 13

az7jh2/SDePER

Spatial Deconvolution method with Platform Effect Removal

Language: Python - Size: 1.42 MB - Last synced at: 28 days ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 1

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: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 0

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

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: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

rockdeme/chrysalis

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

Language: Jupyter Notebook - Size: 67.6 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 0

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: 2 months ago - Pushed at: 3 months ago - Stars: 403 - Forks: 68

LieberInstitute/spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

Language: R - Size: 263 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 93 - Forks: 20

ZJUFanLab/SpaTalk

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

Language: R - Size: 9.83 MB - Last synced at: 6 days ago - Pushed at: 6 months ago - Stars: 71 - Forks: 18

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: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 0

mahmoodlab/HEST

Integrating histology and spatial transcriptomics - NeurIPS 2024

Language: Python - Size: 36.2 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 278 - Forks: 24

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: 2 months ago - Pushed at: 2 months ago - Stars: 64 - Forks: 6

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: 2 months ago - Pushed at: about 3 years ago - Stars: 35 - Forks: 8

kharchenkolab/Baysor

Bayesian Segmentation of Spatial Transcriptomics Data

Language: Julia - Size: 2.12 MB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 174 - Forks: 33

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: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

ddiez/singleCellHaystack-py

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

Language: Python - Size: 69 MB - Last synced at: 10 days ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 1

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: about 1 month ago - Pushed at: 5 months ago - Stars: 22 - Forks: 4

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: 3 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 1

tare/Splotch

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

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

lima1/sttkit

Pipeline for SpatialTranscriptomics and 10X Visium data

Language: R - Size: 648 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 21 - Forks: 7

theMILOlab/SPATA2

A Toolbox for Spatial Transcriptomics Analysis

Language: R - Size: 1.04 GB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 142 - Forks: 20

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: 11 days ago - Pushed at: 7 months ago - Stars: 4 - Forks: 0

MargoKapustina/XeniumSpatialAnalysis

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

Language: R - Size: 374 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 17 - Forks: 2

yintz/SPACEmapX

SPACEmapX

Language: R - Size: 12.5 MB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 3 - Forks: 0

KalinNonchev/azimuthpy

Annotate your single-cell data using Azimuth in python.

Language: Jupyter Notebook - Size: 26.4 KB - Last synced at: 28 days ago - Pushed at: 3 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: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

saezlab/mistyR

Multiview Intercellular SpaTial modeling framework

Language: R - Size: 126 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 54 - Forks: 11

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: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

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: 25 days ago - Pushed at: 6 months ago - Stars: 6 - Forks: 0

doganlab/scmags

Marker Gene Selection Tool For Spatial Transcriptomics

Language: Python - Size: 29.5 MB - Last synced at: 7 days ago - Pushed at: 10 months ago - Stars: 8 - Forks: 1

ma-compbio/SpiceMix

spatial transcriptome, single cell

Language: Jupyter Notebook - Size: 19.1 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 68 - Forks: 8

mehdiborji/nanoranger

simplified cellranger for long-read data

Language: Python - Size: 50.3 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 18 - Forks: 5

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: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0