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: 6.96 MB - Last synced: about 4 hours ago - Pushed: about 5 hours ago - Stars: 39 - Forks: 12

TheJacksonLaboratory/STQ

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

Language: Python - Size: 3.54 MB - Last synced: about 11 hours ago - Pushed: about 22 hours ago - Stars: 9 - Forks: 0

yintz/SPACEmapX

SPACEmapX

Language: R - Size: 213 KB - Last synced: about 12 hours ago - Pushed: 1 day ago - Stars: 1 - Forks: 0

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: about 13 hours ago - Pushed: 1 day ago - Stars: 10 - Forks: 0

gustaveroussy/CFS

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

Language: R - Size: 21.8 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 6 - Forks: 2

bm2-lab/SpaDo

Multi-slice Spatial Transcriptome Domain Analysis.

Language: R - Size: 2.63 MB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 7 - Forks: 0

JEFworks-Lab/SEraster

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

Language: R - Size: 20.6 MB - Last synced: about 20 hours ago - Pushed: 1 day ago - Stars: 4 - Forks: 1

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

A Julia package for single cell and spatial data analysis

Language: Julia - Size: 126 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 5 - Forks: 1

HaojiaWu/CellScopes.jl

A Julia package for single cell and spatial data analysis

Language: Julia - Size: 126 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 17 - Forks: 2

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: 82.6 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 1 - Forks: 0

saezlab/decoupler-py

Python package to perform enrichment analysis from omics data.

Language: Python - Size: 68.9 MB - Last synced: about 12 hours ago - Pushed: 2 days ago - Stars: 139 - Forks: 20

OmicsML/dance

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

Language: Python - Size: 2.08 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 324 - Forks: 30

qiaochen/tranSpa

Translation-based spatial transcriptomics analysis

Language: Python - Size: 2.24 MB - Last synced: 1 day ago - Pushed: 29 days ago - Stars: 4 - Forks: 0

gustaveroussy/sopa

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

Language: Python - Size: 13.5 MB - Last synced: about 12 hours ago - Pushed: 1 day ago - Stars: 67 - Forks: 7

lima1/sttkit

Pipeline for SpatialTranscriptomics and 10X Visium data

Language: R - Size: 541 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 19 - Forks: 7

az7jh2/SDePER_Analysis

This Github repository holds Notebooks and results of running SDePER on both Simulated and Real datasets, and Notebooks for Figure Panels in manuscript.

Language: HTML - Size: 124 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 1 - Forks: 2

kharchenkolab/numbat

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

Language: R - Size: 367 MB - Last synced: about 1 hour ago - Pushed: 13 days ago - Stars: 152 - Forks: 22

jianhuupenn/TESLA

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

Language: Jupyter Notebook - Size: 20.6 MB - Last synced: 1 day ago - Pushed: about 2 months ago - Stars: 38 - Forks: 10

aristoteleo/spateo-viewer

Web application demonstrating 3D modeling of spatial transcriptomics

Language: Python - Size: 621 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 10 - Forks: 3

AlexsLemonade/scpca-nf

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

Language: R - Size: 3.46 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 12 - Forks: 2

LieberInstitute/spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

Language: R - Size: 187 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 72 - Forks: 15

az7jh2/SDePER

Spatial Deconvolution method with Platform Effect Removal

Language: Python - Size: 599 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 1

scverse/squidpy

Spatial Single Cell Analysis in Python

Language: Python - Size: 9.43 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 392 - Forks: 71

Dana-Farber-AIOS/pathml

Tools for computational pathology

Language: Python - Size: 218 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 364 - Forks: 78

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: 7 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 0

alexisvdb/singleCellHaystack

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

Language: R - Size: 78.2 MB - Last synced: 3 days ago - Pushed: 2 months ago - Stars: 73 - Forks: 8

shiquan/Yano

Spatial dissimilarity analysis in single cells

Language: C - Size: 354 KB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0

mehdiborji/nanoranger

simplified cellranger for long-read data

Language: Python - Size: 50.4 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 13 - Forks: 3

mckellardw/DWM_utils

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

Language: Python - Size: 60.1 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 1 - Forks: 3

genecell/COSG

Accurate and fast cell marker gene identification with COSG

Language: Jupyter Notebook - Size: 53.3 MB - Last synced: 14 days ago - Pushed: 12 months ago - Stars: 35 - Forks: 6

HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite

Develop custom oligo design pipelines.

Language: Python - Size: 233 MB - Last synced: about 14 hours ago - Pushed: 1 day ago - Stars: 12 - Forks: 2

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: 50.9 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 1

StatBiomed/SpatialDM

Spatial direct messaging detected by bivariate Moran

Language: Jupyter Notebook - Size: 53.1 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 19 - Forks: 4

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: 11 days ago - Pushed: 7 months ago - Stars: 178 - Forks: 53

sggao/CellSNAP

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

Language: Jupyter Notebook - Size: 111 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 2 - 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: 19 days ago - Pushed: 19 days ago - Stars: 1 - Forks: 0

diegommcc/SpatialDDLS

Deconvolution of spatial transcriptomics data based on Deep Learning

Language: R - Size: 131 MB - Last synced: 17 days ago - Pushed: 20 days ago - Stars: 2 - Forks: 1

hannshu/stCluster

Accurate spatial domain deciphering for spatially resolved transcriptomics with stCluster

Language: Python - Size: 27.2 MB - Last synced: 20 days ago - Pushed: 20 days 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: 21 days ago - Pushed: 21 days ago - Stars: 0 - Forks: 0

pachterlab/voyager

From geospatial to spatial -omics

Language: R - Size: 4.1 GB - Last synced: 25 days ago - Pushed: 26 days ago - Stars: 60 - Forks: 6

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: 6 days ago - Pushed: 6 months ago - Stars: 14 - Forks: 7

kharchenkolab/Baysor

Bayesian Segmentation of Spatial Transcriptomics Data

Language: Julia - Size: 1010 KB - Last synced: 26 days ago - Pushed: 27 days ago - Stars: 127 - Forks: 26

YangLabHKUST/STitch3D

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

Language: Python - Size: 11.1 MB - Last synced: 25 days ago - Pushed: 6 months ago - Stars: 40 - Forks: 2

aristoteleo/spateo-release

Spatiotemporal modeling of spatial transcriptomics

Language: Python - Size: 32.9 MB - Last synced: 6 days ago - Pushed: about 1 month ago - Stars: 145 - Forks: 23

MicTott/SpotSweeper

Spatially-aware quality control for spatial transcriptomics

Language: R - Size: 27.8 MB - Last synced: 14 days ago - Pushed: 27 days ago - Stars: 0 - Forks: 0

rajewsky-lab/openst

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

Language: HTML - Size: 170 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 25 - Forks: 7

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: 16 days ago - Pushed: 7 months ago - Stars: 17 - Forks: 3

gao-lab/SLAT

Spatial-Linked Alignment Tool

Language: Python - Size: 345 MB - Last synced: 15 days ago - Pushed: 5 months ago - Stars: 61 - Forks: 7

smcclatchy/spatial-transcriptomics

Language: R - Size: 59 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 2

jinworks/CellChat

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

Language: R - Size: 63.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 144 - Forks: 14

limin321/stmut

Visualizing Somatic Alterations of 10X Spatial Transcriptomics Data

Language: R - Size: 42.2 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 3 - Forks: 2

saezlab/mistyR

Multiview Intercellular SpaTial modeling framework

Language: R - Size: 126 MB - Last synced: about 13 hours ago - Pushed: about 2 months ago - Stars: 39 - Forks: 9

rockdeme/chrysalis

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

Language: Jupyter Notebook - Size: 54.9 MB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 14 - Forks: 0

MargoKapustina/XeniumSpatialAnalysis

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

Language: R - Size: 269 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 1

acycliq/pciSeq

A probabilistic cell typing algorithm for spatial transcriptomics.

Language: Python - Size: 171 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 22 - Forks: 8

Boli-trainee/Awesome-Deep-Learning-in-Spatial-Transcriptomics

Awesome Deep Learning Methods in Spatial Transcriptomics

Size: 25.4 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 5 - Forks: 0

phipsonlab/spaceMarker

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

lmweber/BestPracticesST

'Best Practices for Spatial Transcriptomics Analysis with Bioconductor' online book

Language: TeX - Size: 111 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 23 - Forks: 7

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: 28 days ago - Pushed: 12 months ago - Stars: 9 - Forks: 0

HayderAminLab/MEA-seqX

Advanced computational framework for integrated analysis of molecular and electrical brain network dynamics at the cellular level

Language: Python - Size: 323 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

agniRS/spatial-RNA-seq

spatial RNA-seq analysis in Glioblastoma using Python

Language: Jupyter Notebook - Size: 16.1 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

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: 2 months ago - Pushed: 2 months ago - Stars: 30 - Forks: 4

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: 2 months ago - Pushed: 2 months ago - Stars: 1 - 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: 648 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

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: 3 months ago - Pushed: about 1 year ago - Stars: 94 - Forks: 20

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: 10 days ago - Pushed: about 2 years ago - Stars: 27 - Forks: 7

Nuwa-genomics/Nuwa

A bioinformatics web app for single cell RNA seq analysis.

Language: Python - Size: 431 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

ch1ru/Nuwa

A bioinformatics web app for single cell RNA seq analysis.

Language: Python - Size: 429 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

wanglab-broad/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 170 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 37 - Forks: 11

OlivierRaineteauSBRI/scRNASeq

Repo linked to our recent publication in Science Advances

Language: HTML - Size: 5.66 GB - Last synced: 4 months ago - Pushed: 4 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: 3.35 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

doganlab/scmags

Marker Gene Selection Tool For Spatial Transcriptomics

Language: Python - Size: 29.5 MB - Last synced: 20 days ago - Pushed: about 2 months ago - Stars: 7 - Forks: 0

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: about 2 months ago - Pushed: over 1 year ago - Stars: 22 - Forks: 2

ZJUFanLab/SpaTalk

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

Language: R - Size: 9.71 MB - Last synced: 3 months ago - Pushed: 11 months ago - Stars: 46 - Forks: 14

CBFLivUni/InflammatorySkinGeoMX

Spatial transcriptomics analysis of inflammatory skin diseases

Language: R - Size: 46.9 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

LieberInstitute/HumanPilot

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

Language: HTML - Size: 289 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 55 - Forks: 27

GuignardLab/napari-sc3D-viewer

A plugin to visualise 3D spatial single cell omics

Language: Python - Size: 38.4 MB - Last synced: 11 days ago - Pushed: about 1 month ago - Stars: 18 - Forks: 2

ZJUFanLab/scCube

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

Language: Jupyter Notebook - Size: 70.9 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 4 - Forks: 0

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

This is repo for the code used in Gift-of-Life paper from Pasca lab

Language: R - Size: 5.59 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 4 - Forks: 1

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: 4 months ago - Pushed: 4 months ago - Stars: 11 - Forks: 1

p4rkerw/Wilson_GBio_2024

Containerized workflow for single cell detection of loss of Y chromosome and other mosaic chromosomal alterations in chronic kidney disease

Language: R - Size: 4.58 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - 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: 3 months ago - Pushed: about 1 year ago - Stars: 30 - Forks: 7

TauConsortium/adad-nucseq-psen1

Repository containing the computational code for the "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: 26 days ago - Pushed: 28 days ago - Stars: 0 - Forks: 0

obendidi/st-visium-datasets

Spatial transcriptomics datasets from 10XGenomices (spatial-gene-expression datasets)

Language: Python - Size: 665 KB - Last synced: 29 days ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

tare/Splotch

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

Language: R - Size: 192 MB - Last synced: about 8 hours ago - Pushed: 4 months ago - Stars: 17 - Forks: 6

ddiez/singleCellHaystack-py

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

Language: Python - Size: 69 MB - Last synced: 4 days ago - Pushed: 4 months ago - Stars: 8 - Forks: 1

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: 43 KB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 3 - Forks: 0

LiuLab-Bioelectronics-Harvard/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 300 MB - Last synced: 5 months ago - Pushed: about 2 years ago - Stars: 6 - Forks: 2

WWXkenmo/ENIGMA

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

Language: HTML - Size: 309 MB - Last synced: 4 months ago - Pushed: 11 months ago - Stars: 25 - Forks: 5

dmcable/spacexr

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

Language: HTML - Size: 537 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 225 - Forks: 65

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: 24.4 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

saezlab/DOT

DOT

Language: R - Size: 27.3 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 4 - Forks: 0

DDDoGGie/RIFF

Pseudo-label supervised graph neural network for robust, fine-grained, interpretable spatial domain identification.

Language: HTML - Size: 25.1 MB - Last synced: 6 months ago - Pushed: 6 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: 377 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 3 - Forks: 0

mckellardw/STRS

Suite of analysis tools for spatial total RNA-sequencing

Language: R - Size: 44 MB - Last synced: about 2 months ago - Pushed: 9 months ago - Stars: 9 - Forks: 2

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: 4 months ago - Pushed: 6 months ago - Stars: 3 - Forks: 0

yanailab/celseq2

Generate the UMI count matrix from CEL-Seq2 sequencing data

Language: Python - Size: 1.34 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 19 - Forks: 13

ZJUFanLab/SpaTrio

Language: Python - Size: 74.5 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 4 - Forks: 1

poloarol/snakemake-vizgen-cell-segmentation

A snakemake pipeline to perform cell segmentation on MERFISH spatial transcriptomics data.

Language: Python - Size: 13.7 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

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: 144 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 45 - Forks: 43