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: about 18 hours ago - Pushed at: about 19 hours 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: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0

HaojiaWu/CellScopes.jl

A Julia package for single cell and spatial data analysis

Language: Julia - Size: 127 MB - Last synced at: 2 days ago - Pushed at: 2 days 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: 3 days ago - Pushed at: 3 days 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: 3 days ago - Pushed at: 3 days ago - Stars: 14 - Forks: 0

cellethology/tic

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

Language: Jupyter Notebook - Size: 104 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 6 - Forks: 0

kharchenkolab/numbat

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

Language: R - Size: 390 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 184 - Forks: 25

AlexsLemonade/scpca-nf

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

Language: R - Size: 4.24 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 14 - Forks: 2

scverse/decoupler

Python package to perform enrichment analysis from omics data.

Language: Python - Size: 99.3 MB - Last synced at: 1 day ago - Pushed at: 9 days ago - Stars: 208 - Forks: 31

HuifangZJU/Vispro

Vispro improves imaging analysis for Visium spatial1 transcriptomics

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

xjtu-omics/STMiner

Language: Python - Size: 110 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 15 - Forks: 7

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: 5 days ago - Pushed at: 5 days ago - Stars: 2 - Forks: 1

Lotfollahi-lab/mintflow

Disentanglement of microenvironment-induced and intrinsic gene expression

Language: Python - Size: 18.5 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 2 - Forks: 0

YangLabHKUST/MCube

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

Language: R - Size: 64.1 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 6 - Forks: 0

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: 40.4 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 201 - Forks: 34

gao-lab/DECIPHER

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

Language: Python - Size: 12.4 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 15 - 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: 2 days ago - Pushed at: 24 days ago - Stars: 24 - Forks: 5

sldyns/SpaHDmap

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

Language: Python - Size: 15.5 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 10 - Forks: 3

MicTott/SpotSweeper

Spatially-aware quality control for spatial transcriptomics

Language: R - Size: 36.9 MB - Last synced at: about 14 hours ago - Pushed at: 6 months ago - Stars: 8 - Forks: 1

KrishnaswamyLab/hypergraph-wavelets

Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics

Language: Python - Size: 1.87 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 2 - Forks: 1

OmicsML/dance

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

Language: Python - Size: 17.7 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 363 - Forks: 38

lmweber/OSTA

"Orchestrating Spatial Transcriptomics Analysis with Bioconductor" book

Language: TeX - Size: 65.7 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 89 - Forks: 31

shiquan/Yano

An R package to perform Spatial dissimilarity analysis in single cells

Language: C - Size: 10.2 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 1 - Forks: 0

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: 153 - Forks: 15

pkosurilab/BellaVista

Python package for interactive visualization of imaging-based spatial transcriptomics

Language: Python - Size: 96.5 MB - Last synced at: 27 minutes ago - Pushed at: 6 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: 12 days ago - Pushed at: 12 days ago - Stars: 22 - Forks: 2

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: 7 days ago - Pushed at: 20 days ago - Stars: 80 - Forks: 7

HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite

Develop custom oligo design pipelines.

Language: Python - Size: 301 MB - Last synced at: 2 days ago - Pushed at: 2 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: 12 days ago - Pushed at: 12 days 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: 13 days ago - Pushed at: 13 days ago - Stars: 1 - Forks: 0

aristoteleo/spateo-release

Spatiotemporal modeling of spatial transcriptomics

Language: Python - Size: 34.1 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 300 - Forks: 39

secrierlab/EnrichMap

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

Language: Python - Size: 89 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 4 - Forks: 0

pachterlab/voyager

From geospatial to spatial -omics

Language: R - Size: 4.32 GB - Last synced at: 11 days ago - Pushed at: 4 months ago - Stars: 95 - Forks: 12

acycliq/pciSeq

A probabilistic cell typing algorithm for spatial transcriptomics.

Language: Python - Size: 173 MB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 24 - Forks: 8

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: 15 days ago - Pushed at: 4 months ago - Stars: 83 - Forks: 50

scverse/squidpy

Spatial Single Cell Analysis in Python

Language: Python - Size: 10.1 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 491 - Forks: 96

ratschlab/DeepSpot

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

Language: Jupyter Notebook - Size: 37 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 48 - Forks: 7

ratschlab/aestetik

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

Language: Python - Size: 27.2 MB - Last synced at: 8 days ago - Pushed at: 20 days ago - Stars: 14 - Forks: 2

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: 12 days ago - Pushed at: over 1 year ago - Stars: 65 - Forks: 4

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: 5 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

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: 27 days ago - Pushed at: 27 days ago - Stars: 6 - Forks: 3

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: 27 days ago - Pushed at: 27 days ago - Stars: 27 - Forks: 2

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: 7.05 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 64 - Forks: 25

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: 29 days ago - Pushed at: 30 days ago - Stars: 2 - Forks: 0

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: 28 days ago - Pushed at: 7 months ago - Stars: 98 - Forks: 17

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: about 1 month ago - Pushed at: about 1 month 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: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

JEFworks-Lab/scatterbar

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

Language: R - Size: 13.2 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 10 - Forks: 1

rockdeme/chrysalis

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

Language: Jupyter Notebook - Size: 67.6 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 17 - Forks: 0

hannshu/stSCI

Joint analysis single-cell and spatial transcriptomics data with stSCI

Language: Python - Size: 9.22 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - 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: about 1 month ago - Pushed at: 2 months ago - Stars: 403 - Forks: 68

Dana-Farber-AIOS/pathml

Tools for computational pathology

Language: Python - Size: 218 MB - Last synced at: 27 days ago - Pushed at: about 2 months ago - Stars: 425 - Forks: 87

LieberInstitute/spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

Language: R - Size: 263 MB - Last synced at: 27 days ago - Pushed at: about 2 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: 1 day ago - Pushed at: 5 months ago - Stars: 71 - Forks: 18

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: about 1 month ago - Pushed at: about 1 month ago - Stars: 36 - Forks: 5

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: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

mahmoodlab/HEST

Integrating histology and spatial transcriptomics - NeurIPS 2024

Language: Python - Size: 36.2 MB - Last synced at: about 1 month ago - Pushed at: about 2 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: about 1 month ago - Pushed at: about 1 month ago - Stars: 64 - 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: about 2 months ago - Stars: 20 - Forks: 7

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: about 1 month 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: about 1 month ago - Pushed at: 7 months ago - Stars: 174 - Forks: 33

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: about 2 months ago - Pushed at: about 2 months ago - Stars: 363 - Forks: 84

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

smcclatchy/spatial-transcriptomics

Language: JavaScript - Size: 1.45 GB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 3

alexisvdb/singleCellHaystack

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

Language: R - Size: 78.2 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 83 - Forks: 9

ddiez/singleCellHaystack-py

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

Language: Python - Size: 69 MB - Last synced at: 11 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: 12 days ago - Pushed at: 4 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: about 2 months ago - Pushed at: about 2 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: 20 days ago - Pushed at: about 1 month ago - Stars: 21 - Forks: 6

lima1/sttkit

Pipeline for SpatialTranscriptomics and 10X Visium data

Language: R - Size: 648 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 21 - Forks: 7

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: about 2 months ago - Stars: 2 - Forks: 0

theMILOlab/SPATA2

A Toolbox for Spatial Transcriptomics Analysis

Language: R - Size: 1.04 GB - Last synced at: about 2 months ago - Pushed at: about 2 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: 10 days ago - Pushed at: 6 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: about 2 months ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 2

StatBiomed/SpatialDM

Spatial direct messaging detected by bivariate Moran

Language: Jupyter Notebook - Size: 51.1 MB - Last synced at: 19 days ago - Pushed at: about 2 months ago - Stars: 26 - Forks: 6

yintz/SPACEmapX

SPACEmapX

Language: R - Size: 12.5 MB - Last synced at: 13 days ago - Pushed at: 13 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: about 1 month ago - Pushed at: 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: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

saezlab/mistyR

Multiview Intercellular SpaTial modeling framework

Language: R - Size: 126 MB - Last synced at: about 2 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: about 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

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: about 16 hours ago - Pushed at: 2 months ago - Stars: 17 - Forks: 5

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: 2 months ago - Pushed at: 5 months ago - Stars: 6 - Forks: 0

doganlab/scmags

Marker Gene Selection Tool For Spatial Transcriptomics

Language: Python - Size: 29.5 MB - Last synced at: 8 days ago - Pushed at: 9 months ago - Stars: 8 - Forks: 1

ma-compbio/SpiceMix

spatial transcriptome, single cell

Language: Jupyter Notebook - Size: 19.1 MB - Last synced at: 18 days ago - Pushed at: over 2 years ago - Stars: 68 - Forks: 8

gao-lab/SLAT

Spatial-Linked Alignment Tool

Language: Python - Size: 334 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 86 - Forks: 10

mehdiborji/nanoranger

simplified cellranger for long-read data

Language: Python - Size: 50.3 MB - Last synced at: 2 months ago - Pushed at: 2 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: 2 months ago - Pushed at: 2 months 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: 2 months ago - Pushed at: 2 months ago - Stars: 3 - Forks: 0

khasrawlab/TILproject

Uncovering Determinants of TIL Expansion in High-Grade Gliomas through Immunophenotyping, TCR Profiling, Single-Cell, Spatial Transcriptomics, and Proeteomics

Language: R - Size: 121 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

genecell/COSG

Accurate and fast cell marker gene identification with COSG

Language: Python - Size: 68.8 MB - Last synced at: 29 days ago - Pushed at: 3 months ago - Stars: 44 - Forks: 8

az7jh2/SDePER

Spatial Deconvolution method with Platform Effect Removal

Language: Python - Size: 1.41 MB - Last synced at: 30 days ago - Pushed at: 8 months ago - Stars: 4 - Forks: 1

QI2lab/merfish3d-analysis

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

Language: Python - Size: 3.52 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 6 - Forks: 3

christinehou11/BatchSVG

Identification of biased features from SVGs in spatial transcriptomics data

Language: R - Size: 15.5 MB - Last synced at: 6 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: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

smorabit/hdWGCNA

High dimensional weighted gene co-expression network analysis

Language: R - Size: 275 MB - Last synced at: 3 months ago - Pushed at: 3 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: 3 months ago - Pushed at: 3 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: 3 months ago - Pushed at: about 3 years ago - Stars: 69 - Forks: 5