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Projects in Awesome Lists tagged with single-cell-analysis

A curated list of projects in awesome lists tagged with single-cell-analysis .

https://github.com/sqjin/CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

cell-cell-communication cell-cell-interaction microenvironment single-cell-analysis

Last synced: 30 Apr 2025

https://github.com/jinworks/cellchat

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

cell-cell-communication cell-cell-interaction microenvironment single-cell-analysis spatial-transcriptomics

Last synced: 14 Jan 2026

https://github.com/satijalab/seurat-wrappers

Community-provided extensions to Seurat

community single-cell-analysis single-cell-genomics

Last synced: 05 Apr 2025

https://github.com/slowkow/harmonypy

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

bioinformatics data-integration data-science single-cell-analysis

Last synced: 24 Apr 2026

https://github.com/pwwang/scplotter

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

single-cell-analysis single-cell-rna-seq single-cell-sequencing visualization

Last synced: 05 Apr 2025

https://github.com/labsyspharm/scimap

Spatial Single-Cell Analysis Toolkit

image-analysis pypi python single-cell-analysis spatial-analysis

Last synced: 12 Feb 2026

https://gregoryschwartz.github.io/too-many-cells/

Cluster single cells and analyze cell clade relationships with colorful visualizations.

bioinformatics-algorithms bioinformatics-pipeline single-cell single-cell-analysis single-cell-rna-seq visualization

Last synced: 09 Apr 2025

https://github.com/JEFworks-Lab/HoneyBADGER

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

bayesian bioinformatics cnv-detection heterogeneity hmm single-cell-analysis single-cell-rna-seq subpopulation transcriptomics

Last synced: 09 Apr 2025

https://github.com/dynverse/dyngen

Simulating single-cell data using gene regulatory networks 📠

benchmarking single-cell single-cell-analysis single-cell-omics

Last synced: 17 Mar 2026

https://github.com/berenslab/umi-normalization

Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology

dimensionality-reduction gene-selection glm-pca negative-binomial negative-binomial-model negative-binomial-regression normalization scrna single-cell-analysis single-cell-rna-seq t-sne umi-count umi-count-matrix

Last synced: 01 Feb 2026

https://github.com/theislab/pseudodynamics

Dynamic models for single-cell RNA-seq time series.

population-dynamics single-cell-analysis single-cell-rna-seq time-series

Last synced: 11 Oct 2025

https://github.com/nasqar/seuratv3wizard

A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3

bioinformatics r seurat shiny shiny-apps single-cell single-cell-analysis single-cell-genomics single-cell-rna-seq visualization webapp

Last synced: 15 Nov 2025

https://github.com/xzhoulab/DRComparison

Comparison of dimensionality reduction methods

dimensionality-reduction single-cell-analysis

Last synced: 11 May 2025

https://github.com/jumphone/beer

BEER: Batch EffEct Remover for single-cell data

batch-effects scatac-seq scrna-seq single-cell-analysis umap

Last synced: 14 May 2025

https://github.com/arogozhnikov/demuxalot

Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing

biotech demultiplexing scrnaseq single-cell-analysis

Last synced: 23 Jul 2025

https://github.com/nasqar/SeuratWizard

This is a web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat.

r seurat shiny shiny-apps single-cell single-cell-analysis single-cell-genomics single-cell-rna-seq webapplication

Last synced: 19 Nov 2025

https://github.com/obophenotype/provisional_cell_ontology

Draft cell type definitions from data - candidates for inclusion in CL

cell-ontology cell-types obofoundry ontology single-cell-analysis single-cell-rna-seq transcriptomics

Last synced: 16 Apr 2026

https://github.com/ocbe-uio/discbio

A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics

biomarker-discovery jupyter-notebook r-package scrna-seq single-cell-analysis transcriptomics

Last synced: 11 Jul 2025

https://github.com/CABSEL/SINCERITIES

SINCERITIES is a tool for inferring gene regulatory networks from time-stamped cross-sectional single cell transcriptional expression profiles.

network-inference single-cell-analysis

Last synced: 09 Apr 2025

https://github.com/jhu99/vipcca

Single-cell alignment

cca non-linear-model python single-cell-analysis

Last synced: 15 Apr 2025

https://github.com/CABSEL/CALISTA

CALISTA: Clustering And Lineage Inference in Single Cell Transcriptional Analysis

network-analysis single-cell-analysis

Last synced: 08 Apr 2025

https://github.com/jumphone/scref

A reference-based solution for single-cell analysis

bioinformatics single-cell-analysis single-cell-rna-seq

Last synced: 27 Feb 2026

https://github.com/rraadd88/htsimaging

🔬Python package for high-throughput single-cell imaging analysis.

microscopy-image-analysis single-cell-analysis

Last synced: 22 Jun 2025

https://github.com/kullrich/oggmap

oggmap is a python package to extract orthologous maps (short: orthomap or in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Oggmap results (gene ages per orthologous group) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

evolution evomed phylogeny phylotranscriptomics single-cell-analysis transcriptomics

Last synced: 01 Mar 2026

https://github.com/hesselberthlab/scrunchy

R toolkit for the analysis of single-cell functional heterogeneity

single-cell-analysis single-cell-rna-seq

Last synced: 05 Feb 2026

https://github.com/euxhenh/grinch

A library for differential expression and gene set enrichment analysis based on hydra and pydantic.

clustering differential-expression-analysis gene-set-enrichment marker-genes single-cell single-cell-analysis

Last synced: 04 Apr 2026

https://github.com/jumphone/gca

GCA: Gene Correlation Analysis for Single-cell RNA-seq data

bioinformatics single-cell single-cell-analysis single-cell-rna-seq

Last synced: 13 Mar 2025

https://github.com/jumphone/scc

Single-Cell Communication Toolkit

single-cell-analysis single-cell-rna-seq

Last synced: 23 Jun 2025

https://github.com/12danielll/neurogenomics_project

This project focuses on analyzing sequencing data to understand molecular mechanisms of neurological diseases and predict the effectiveness of immunotherapy in breast cancer patients. It integrates Python and R scripts for data processing, statistical analysis, and visualization, alongside a comprehensive report detailing methods and findings.

bioinformatics biostatistics clustering clustering-algorithms data-analysis data-visualization deseq2 differential-gene-expression functional-analysis immune-therapy machine-learning neurological-disease neuroscience pca-analysis python r seurat single-cell-analysis

Last synced: 06 Apr 2026