jamesjcai/scGEAToolbox

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

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scRNA-tools/scRNA-tools

Table of software for the analysis of single-cell RNA-seq data.

Language: R - Size: 128 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 319 - Forks: 77

theislab/zellkonverter

Conversion between scRNA-seq objects

Language: R - Size: 2.02 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 171 - Forks: 29

Oshlack/splatter

Simple simulation of single-cell RNA sequencing data

Language: R - Size: 57.2 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 226 - Forks: 57

mtvector/scANTIPODE

Variational Inference for Cell Type Evolution

Language: Python - Size: 357 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0

interactivereport/cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

Language: Jupyter Notebook - Size: 162 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 146 - Forks: 49

quadbio/cell-annotator

Automatically annotate cell types, consistently across samples.

Language: Python - Size: 2.4 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 10 - Forks: 1

scverse/scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

Language: Python - Size: 148 MB - Last synced at: 2 days ago - Pushed at: 7 days ago - Stars: 1,362 - Forks: 385

malbiruk/plotly_for_scanpy

A collection of Plotly-based functions to visualize Scanpy data mimicking functions from scanpy.pl package.

Language: Python - Size: 94.7 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

snaketron/scBubbletree

scBubbletree: quantitative tool for visual exploration of scRNA-seq data

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dputhier/scigenex

This repository stores the scigenex R library.

Language: R - Size: 75.7 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 4 - Forks: 2

epigen/genome_tracks

A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.

Language: Python - Size: 118 KB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 23 - Forks: 1

broadinstitute/Tangram

Spatial alignment of single cell transcriptomic data.

Language: Jupyter Notebook - Size: 141 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 288 - Forks: 55

dpeerlab/Palantir

Single cell trajectory detection

Language: Jupyter Notebook - Size: 56.2 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 242 - Forks: 52

AlexsLemonade/scpca-nf

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

Language: R - Size: 4.01 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 13 - Forks: 2

nf-core/scnanoseq

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

Language: Nextflow - Size: 40.5 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 34 - Forks: 10

mdozmorov/scRNA-seq_notes

A list of scRNA-seq analysis tools

Language: R - Size: 1.9 MB - Last synced at: 7 days ago - Pushed at: about 2 months ago - Stars: 691 - Forks: 154

Teichlab/celltypist

A tool for semi-automatic cell type classification

Language: Python - Size: 22 MB - Last synced at: 10 days ago - Pushed at: 27 days ago - Stars: 351 - Forks: 45

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: 9 days ago - Pushed at: about 2 months ago - Stars: 79 - Forks: 50

single-cell-genetics/vireo

Demultiplexing pooled scRNA-seq data with or without genotype reference

Language: Python - Size: 4.39 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 83 - Forks: 28

meyer-lab/barcoded-Pf2

Pf2 exploration of cell-to-cell heterogeneity with barcoded cell lines.

Language: Jupyter Notebook - Size: 27.1 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0

elolab/Coralysis

A multi-level integration algorithm for sensitive integration, reference-mapping, and cell state identification in single-cell data.

Language: R - Size: 25.3 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 1 - Forks: 0

biobenkj/compartmap

Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq

Language: R - Size: 73 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 14 - Forks: 10

PMBio/Health-Privacy-Challenge

The starter kit for the CAMDA 2025 Health Privacy Challenge.

Language: Python - Size: 43 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 5 - Forks: 5

scverse/muon

muon is a multimodal omics Python framework

Language: Python - Size: 5.05 MB - Last synced at: 8 days ago - Pushed at: about 2 months ago - Stars: 231 - Forks: 31

chanzuckerberg/cellxgene

An interactive explorer for single-cell transcriptomics data

Language: JavaScript - Size: 239 MB - Last synced at: 10 days ago - Pushed at: 14 days ago - Stars: 667 - Forks: 132

Qile0317/APackOfTheClones

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles.

Language: R - Size: 178 MB - Last synced at: 7 days ago - Pushed at: 5 months ago - Stars: 16 - Forks: 2

BgeeDB/BgeeDB_R

Source code of the R packge BgeeDB to use data from the Bgee database

Language: R - Size: 576 KB - Last synced at: 11 days ago - Pushed at: 3 months ago - Stars: 16 - Forks: 6

epigen/dea_limma

A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.

Language: R - Size: 147 KB - Last synced at: 6 days ago - Pushed at: about 2 months ago - Stars: 26 - Forks: 2

epigen/scrnaseq_processing_seurat

A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.

Language: R - Size: 1.27 MB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 22 - Forks: 0

epigen/mixscape_seurat

A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.

Language: R - Size: 113 KB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 19 - Forks: 2

epigen/dea_seurat

A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.

Language: R - Size: 358 KB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 21 - Forks: 11

bnediction/scBoolSeq

scBoolSeq: scRNA-Seq data binarisation and synthetic generation from Boolean dynamics

Language: Python - Size: 254 KB - Last synced at: 11 days ago - Pushed at: 3 months ago - Stars: 10 - Forks: 1

Harkany-Lab/Gueissaz_2025

This repository contains code to identify expression patterns of genes and cells involved in hypothalamic control of metabolism and stress response. It also performs bioinformatic molecular profile analysis of parvocellular and preautonomic neurons i.e. Crh. Overall, it enables reproducible analysis of biomarkers and ALK / Augα signaling in PVH

Language: BibTeX Style - Size: 119 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 0 - Forks: 0

samuel-marsh/scCustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

Language: R - Size: 305 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 248 - Forks: 24

yxwucq/scExtract

Automatic annotation of single-cell RNA-seq data from the literature

Language: Python - Size: 20.5 MB - Last synced at: 16 days ago - Pushed at: 17 days ago - Stars: 5 - Forks: 0

HaojiaWu/CellScopes.jl

A Julia package for single cell and spatial data analysis

Language: Julia - Size: 126 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 34 - Forks: 3

Novartis/cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

Language: Python - Size: 203 KB - Last synced at: 18 days ago - Pushed at: about 1 year ago - Stars: 61 - Forks: 34

liulab-dfci/MAESTRO

Single-cell Transcriptome and Regulome Analysis Pipeline

Language: C - Size: 203 MB - Last synced at: 8 days ago - Pushed at: about 2 years ago - Stars: 279 - Forks: 78

ZJUFanLab/scDeepSort

Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

Language: Python - Size: 19.4 MB - Last synced at: 4 days ago - Pushed at: almost 2 years ago - Stars: 103 - Forks: 19

jiang-junyao/CACIMAR

cross-species analysis of cell identities, markers and regulations

Language: R - Size: 111 MB - Last synced at: 12 days ago - Pushed at: 20 days ago - Stars: 12 - Forks: 4

AntonioDeFalco/SCEVAN

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

Language: HTML - Size: 63 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 100 - Forks: 25

jr-leary7/scLANE-Revision

code and data relating to the scLANE revision

Language: HTML - Size: 411 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 0 - Forks: 0

liuzj039/jpy_tools

Language: Jupyter Notebook - Size: 270 MB - Last synced at: 21 days ago - Pushed at: 22 days ago - Stars: 9 - Forks: 0

Teichlab/Genes2Genes

Aligning gene expression trajectories of single-cell reference and query systems

Language: Jupyter Notebook - Size: 34.5 MB - Last synced at: 12 days ago - Pushed at: 6 months ago - Stars: 63 - Forks: 8

PMBio/MuDataSeurat

.h5mu files interface for Seurat

Language: R - Size: 3.98 MB - Last synced at: 11 days ago - Pushed at: over 1 year ago - Stars: 29 - Forks: 13

sanderlab/scPerturb

scPerturb: A resource and a python/R tool for single-cell perturbation data

Language: Jupyter Notebook - Size: 209 MB - Last synced at: 12 days ago - Pushed at: about 2 months ago - Stars: 118 - Forks: 7

stefanpeidli/mousipy

Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.

Language: Jupyter Notebook - Size: 14.9 MB - Last synced at: 14 days ago - Pushed at: 6 months ago - Stars: 20 - Forks: 5

ylaboratory/ALPINE

ALPINE is a semi-supervised non-negative matrix factorization (NMF) framework designed to effectively distinguish between multiple phenotypic conditions based on shared biological factors, while also providing direct interpretability of condition-associated genes. The preprint is available on bioRxiv.

Language: Python - Size: 1.03 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 2 - Forks: 1

JCVenterInstitute/FRmatch

Cell type matching in single-cell RNA-sequencing data using FR-Match

Language: R - Size: 156 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 19 - Forks: 3

theislab/scgen

Single cell perturbation prediction

Language: Python - Size: 69.3 MB - Last synced at: 19 days ago - Pushed at: 5 months ago - Stars: 286 - Forks: 58

jr-leary7/bayesVG

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

Language: R - Size: 15.7 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 0 - Forks: 0

wukevin/babel

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

Language: Jupyter Notebook - Size: 316 MB - Last synced at: 12 days ago - Pushed at: almost 2 years ago - Stars: 41 - Forks: 16

AlicenJoyHenning/DamageToolReviewArticle

🗒️ Analysis scripts for the methods outlined in our review article evaluating scRNA-seq damaged cell detection strategies

Language: Jupyter Notebook - Size: 21.1 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 0 - Forks: 0

parashardhapola/scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Language: Python - Size: 32.8 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 100 - Forks: 12

Bayer-Group/cellenium

Cellenium is a FAIR and scalable interactive visual analytics app for scRNA-Seq data (single-cell RNA sequencing).

Language: Jupyter Notebook - Size: 12.4 MB - Last synced at: 9 days ago - Pushed at: over 1 year ago - Stars: 27 - Forks: 5

evan950608/NYCU_BMI_scRNA_study

Source code for the study "Marker Gene Identification Algorithm of Precision Clustering for Single-Cell Sequencing," conducted at the Institute of Biomedical Informatics, National Yang Ming Chiao Tung University (NYCU BMI) by Zhe-Yuan Li, published in January 2025.

Language: Jupyter Notebook - Size: 1.89 GB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 0 - Forks: 0

Japrin/scPip

A pipeline for scRNA-seq data analysis

Language: R - Size: 4.5 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 12 - Forks: 1

dpeerlab/Harmony

Harmony framework for connecting scRNA-seq data from discrete time points

Language: Jupyter Notebook - Size: 5.34 MB - Last synced at: 7 days ago - Pushed at: 9 months ago - Stars: 47 - Forks: 12

Teichlab/cellhint

A tool for semi-automatic cell type harmonization and integration

Language: Python - Size: 6.78 MB - Last synced at: 9 days ago - Pushed at: 29 days ago - Stars: 102 - Forks: 14

wisdomadingo/scRNAseq_Exosome

scRNA-seq analysis of exosomes

Language: R - Size: 1.65 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

pachterlab/kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

Language: Python - Size: 226 MB - Last synced at: 13 days ago - Pushed at: about 1 month ago - Stars: 160 - Forks: 24

scapeML/scape

Single-cell Analysis of Perturbational Effects using Machine Learning

Language: Python - Size: 3.13 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 3

BimberLab/nimble

nimble — execute lightweight, flexible alignments on custom reference libraries

Language: Python - Size: 278 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

theislab/cpa

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

Language: Python - Size: 54.1 MB - Last synced at: 20 days ago - Pushed at: 8 months ago - Stars: 97 - Forks: 16

jr-leary7/scLANE

Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.

Language: R - Size: 31.3 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 10 - Forks: 3

lilab-bcb/cirrocumulus

Bring your single-cell data to life

Language: JavaScript - Size: 223 MB - Last synced at: 15 days ago - Pushed at: about 2 months ago - Stars: 79 - Forks: 16

BaderLab/scClustViz

Explore and share your scRNAseq clustering results

Language: R - Size: 696 MB - Last synced at: 17 days ago - Pushed at: over 1 year ago - Stars: 50 - Forks: 9

kharchenkolab/pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

Language: JavaScript - Size: 78.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 223 - Forks: 47

dyammons/canine-blood-VS-tils-scrna

This GitHub repository contains all the analysis code used in, "Characterization of canine tumor-infiltrating leukocyte transcriptomic signatures reveals conserved expression patterns with human osteosarcoma."

Language: R - Size: 2.05 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

vanallenlab/beanie

Tool for group biology estimation in single-cell RNAseq data

Language: Python - Size: 21.5 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 1

Japrin/sscVis

simpler single cell RNAseq data Visualization

Language: R - Size: 116 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 7 - Forks: 3

JackNg88/VARACS

Visualization Analysis of RNAseq,ATACseq,Chipseq and ScRNAseq

Language: Python - Size: 5.86 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0

ilia-kats/MuData

MuData-compatible storage for bioconductor's MultiAssayExperiment

Language: R - Size: 8.58 MB - Last synced at: 10 days ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 4

Gartner-Lab/deMULTIplex2

deMULTIplex2: robust sample demultiplexing for scRNA-seq

Language: R - Size: 15.9 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 0

immunogenomics/symphony

Efficient and precise single-cell reference atlas mapping with Symphony

Language: Jupyter Notebook - Size: 124 MB - Last synced at: 23 days ago - Pushed at: about 2 years ago - Stars: 103 - Forks: 22

JonathanShor/DoubletDetection

Doublet detection in single-cell RNA-seq data.

Language: Python - Size: 8.05 MB - Last synced at: 13 days ago - Pushed at: 2 months ago - Stars: 91 - Forks: 23

Zilong-Li/PCAone

Fast, Accurate and Memory-Efficient Principal Component Analysis All in One

Language: C++ - Size: 6.42 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 45 - Forks: 3

Aavache/awesome-genetic-ai-papers

Recent awesome AI papers about genomics.

Size: 9.77 KB - Last synced at: 8 days ago - Pushed at: 12 months ago - Stars: 1 - Forks: 1

devCellPy-Team/devCellPy

devCellPy is a Python package designed for hierarchical multilayered classification of cells based on single-cell RNA-sequencing.

Language: Jupyter Notebook - Size: 88.7 MB - Last synced at: 10 days ago - Pushed at: about 1 year ago - Stars: 25 - Forks: 3

Iwo-K/genespector

Language: Python - Size: 4.65 MB - Last synced at: 3 days ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 2

PeijingZhang/Shennong

A deep-learning framework to predict the tumor-associated cells' reaction to pharmacologic perturbations at the single-cell level.

Language: Python - Size: 44.7 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

ZJUFanLab/scDeepSort_performance_comparison

The source code and results for different methods on annotating external testing datsets of human and mouse.

Language: R - Size: 6.33 MB - Last synced at: 4 days ago - Pushed at: about 4 years ago - Stars: 12 - Forks: 0

jhudsl/GDSCN_Book_Statistics_for_Genomics_scRNA-seq

A set of lab modules for single cell RNA-seq analysis

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BgeeDB/BgeeCall

Source code of the BgeeCall R package, for automatic RNA-Seq present/absent gene expression calls generation

Language: R - Size: 24.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 1

single-cell-genetics/cardelino

Clone identification from single-cell data

Language: R - Size: 9.8 MB - Last synced at: 11 days ago - Pushed at: over 2 years ago - Stars: 61 - Forks: 13

eleozzr/desc

Deep Embedding for Single-cell Clustering

Language: Jupyter Notebook - Size: 168 MB - Last synced at: 2 days ago - Pushed at: about 1 year ago - Stars: 84 - Forks: 25

neurogenomics/RareDiseasePrioritisation

Prioritise cell-type-specific gene targets from the Rare Disease Celltyping project.

Language: HTML - Size: 77.9 MB - Last synced at: 19 days ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

htejedam/SankeyPlot_CellChat

Generate Sankey plots from merged CellChat objects

Size: 0 Bytes - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Starlitnightly/scltnn

A composite regression neural network for latent timing prediction of single-cell RNA-seq data

Language: Jupyter Notebook - Size: 151 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 5 - Forks: 2

RIPKEL/Endoderm_Organogenesis

Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution

Language: R - Size: 306 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

jr-leary7/bayesHVG

Identify highly variables genes in scRNA-seq data using Bayesian inference.

Language: R - Size: 122 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

auroramaurizio/my_RNA_seq_pipelines

my_RNA_seq_pipelines

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junjunlab/scRNAtoolVis

Useful functions to make your scRNA-seq plot more cool!

Language: R - Size: 22.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 304 - Forks: 30

VCCRI/Sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data

Language: R - Size: 19.9 MB - Last synced at: 11 days ago - Pushed at: almost 2 years ago - Stars: 50 - Forks: 17

jumphone/BEER

BEER: Batch EffEct Remover for single-cell data

Language: R - Size: 60.1 MB - Last synced at: 19 days ago - Pushed at: 3 months ago - Stars: 24 - Forks: 9

theislab/scarches

Reference mapping for single-cell genomics

Language: Jupyter Notebook - Size: 825 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 347 - Forks: 52

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: 9 days ago - Pushed at: 3 months ago - Stars: 6 - Forks: 3

saeyslab/multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

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martabica/breast-cancer-atlas-metadata-curation

This repository is dedicated to curating, organizing, and annotating metadata for scRNA-seq datasets of human breast cancer, with a focus on datasets that include myeloid cells. This work is tied to the Mye-InfoBank project, aiming to enhance data integration, analysis, and reproducibility in breast cancer

Size: 0 Bytes - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0