Projects in Awesome Lists tagged with single-cell-genomics
A curated list of projects in awesome lists tagged with single-cell-genomics .
https://github.com/satijalab/seurat
R toolkit for single cell genomics
cran human-cell-atlas single-cell-genomics single-cell-rna-seq
Last synced: 15 May 2025
https://github.com/scverse/scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
cite-seq deep-generative-model deep-learning human-cell-atlas scrna-seq scverse single-cell-genomics single-cell-rna-seq variational-autoencoder variational-bayes
Last synced: 13 May 2025
https://github.com/scverse/squidpy
Spatial Single Cell Analysis in Python
data-visualization image-analysis single-cell-genomics single-cell-rna-seq spatial-analysis spatial-transcriptomics squidpy
Last synced: 07 May 2025
https://github.com/theislab/cellrank
CellRank: dynamics from multi-view single-cell data
bioinformatics cell-fate-determination cell-fate-transitions data-science fuzzy-clustering-analyses genetics machine-learning manifold-learning markov-chains rna-velocity single-cell-genomics single-cell-rna-seq trajectory-generation
Last synced: 01 May 2025
https://github.com/theislab/scarches
Reference mapping for single-cell genomics
batch-correction data-integration deep-learning human-cell-atlas multimodal-deep-learning multiomics rna-seq-analysis scrna-seq single-cell single-cell-genomics
Last synced: 28 Nov 2024
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/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.
customization ggplot2 scrna-seq seurat single-cell single-cell-genomics single-cell-rna-seq visualization
Last synced: 15 May 2025
https://github.com/mojaveazure/seurat-disk
Interfaces for HDF5-based Single Cell File Formats
hdf5-format single-cell-genomics single-cell-rna-seq
Last synced: 19 Dec 2024
https://github.com/satijalab/seurat-data
Dataset distribution for Seurat
datasets single-cell single-cell-genomics
Last synced: 05 Apr 2025
https://github.com/satijalab/azimuth
A Shiny web app for mapping datasets using Seurat v4
shiny-app single-cell-genomics single-cell-rna-seq
Last synced: 01 Mar 2025
https://github.com/yanwu2014/swne
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
bioinformatics data-visualization dimensionality-reduction nonnegative-matrix-factorization single-cell-analysis single-cell-atac-seq single-cell-genomics single-cell-rna-seq statistical-methods
Last synced: 09 Apr 2025
https://github.com/calico/scnym
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
adversarial-training rna-seq semi-supervised single-cell single-cell-genomics
Last synced: 28 Nov 2024
https://github.com/mojaveazure/loomr
An R-based interface for loom files
hdf5 loom loom-files r single-cell-genomics single-cell-rna-seq
Last synced: 14 Apr 2025
https://github.com/robertaboukhalil/ginkgo
Cloud-based single-cell copy-number variation analysis tool
bioinformatics sequencing single-cell-genomics
Last synced: 29 Apr 2025
https://github.com/broadinstitute/single_cell_portal
Tutorials, workflows, and convenience scripts for Single Cell Portal
human-cell-atlas rna-seq-analysis single-cell-genomics
Last synced: 20 Feb 2025
https://github.com/pinellolab/pyrovelocity
š¯’«robabilistic modeling of RNA velocity ā¬±
cell-fate-determination deep-generative-model developmental-trajectories multiomics probabilistic-models probabilistic-programming pyro rna-splicing rna-splicing-analysis rna-velocity rna-velocity-estimation single-cell-genomics single-cell-multiomics single-cell-rna-seq transcriptomics
Last synced: 07 May 2025
https://github.com/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.
clonal-analysis immune-repertoire immune-system r scrna-seq scrnaseq seurat single-cell single-cell-genomics
Last synced: 10 Apr 2025
https://github.com/asmagen/robustsinglecell
Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.
clustering data-integration scrnaseq single-cell-genomics single-cell-rna-seq
Last synced: 23 Mar 2025
https://github.com/asmagen/robustSingleCell
Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.
clustering data-integration scrnaseq single-cell-genomics single-cell-rna-seq
Last synced: 08 Apr 2025
https://github.com/krasnitzlab/scgv
SCGV is an interactive graphical tool for single-cell genomics data, with emphasis on single-cell genomics of cancer
genomics genomics-visualization single-cell single-cell-genomics
Last synced: 12 Apr 2025
https://github.com/satijalab/seurat-docker
Docker images of Seurat
docker human-cell-atlas single-cell single-cell-analysis single-cell-genomics
Last synced: 03 May 2025
https://github.com/drisso/archive-zinbwave
Archived version of the zinbwave package. All future development will be done on https://github.com/drisso/zinbwave
gene-expression r rna-seq single-cell single-cell-genomics statistical-models
Last synced: 02 Jan 2025
https://github.com/laminetourelab/singlecell-rnaseq-tools
This repository contains single cell analysis pipelines.
cellrank expimap rnavelocity scvelo single-cell single-cell-analysis single-cell-genomics single-cell-rna-seq velocity
Last synced: 01 Jan 2025
https://github.com/neurogenomics/rarediseaseprioritisation
Prioritise cell-type-specific gene targets from the Rare Disease Celltyping project.
aav celltypes clinical-research genomics rare-disease scrna-seq single-cell-genomics
Last synced: 03 Apr 2025
https://github.com/grimbough/tenxbenchmarking
Benchmarking R & Bioconductor performance working with large-scale single-cell data
hdf5 r single-cell-genomics tenxgenomics
Last synced: 29 Mar 2025
https://github.com/krasnitzlab/scclust
Segmentation and Clustering of Single Cell Sequencing Copy Number Profiles
clustering r segmentation single-cell-genomics
Last synced: 26 Mar 2025