dynverse: benchmarking, constructing and interpreting single-cell trajectories

All

129 repositories

anndata
Public
Annotated multivariate observation data in R
R
•
Other
•4•43•6•1•Updated Nov 15, 2024Nov 15, 2024
dyngen
Public
Simulating single-cell data using gene regulatory networks 📠
benchmarking single-cell single-cell-analysis single-cell-omics
HTML
•
Other
•6•73•18•1•Updated Feb 21, 2024Feb 21, 2024
babelwhale
Public
Talking to Docker and Singularity containers
R
•
Other
•6•24•2•1•Updated Dec 27, 2023Dec 27, 2023
dynmethods
Public
A collection of 50+ trajectory inference methods within a common interface 📥📤
bioinformatics-algorithms single-cell-rna-seq single-cell-analysis trajectory-inference pseudotemporal-ordering trajectory-inference-methods
R
•
Other
•26•120•19•0•Updated Dec 21, 2023Dec 21, 2023
lmds
Public
Landmark Multi-Dimensional Scaling
R
•1•8•2•0•Updated Sep 22, 2023Sep 22, 2023
dynbenchmark
Public
Comparison of methods for trajectory inference on single-cell data 🥇
benchmarking bioinformatics-algorithms trajectory-inference
R
•
Other
•41•199•4•0•Updated Aug 30, 2023Aug 30, 2023
dynwrap
Public
A common data format and inference environment for single-cell trajectories 📦
trajectory-inference
R
•
Other
•7•15•17•0•Updated Jul 18, 2023Jul 18, 2023
dynfeature
Public
Extracting relevant features from single-cell trajectories 🎯
R
•
Other
•3•0•0•0•Updated Mar 1, 2023Mar 1, 2023
dynutils
Public
Common Functionality for the 'dynverse' Packages
R
•
Other
•2•3•0•0•Updated Oct 6, 2022Oct 6, 2022
dynplot2
Public
A grammar of graphics for single-cell trajectories 📈
R
•0•0•2•1•Updated Dec 16, 2021Dec 16, 2021
dynio
Public
R
•
Other
•0•0•0•0•Updated Dec 10, 2021Dec 10, 2021
ti_slingshot
Public
R
•
Other
•4•0•2•0•Updated Dec 10, 2021Dec 10, 2021
dynplot
Public
Visualising single-cell trajectories, including comparisons between two models 📈
visualisation trajectory-inference
R
•
Other
•5•30•10•0•Updated Dec 9, 2021Dec 9, 2021
dynbenchmark_results
Public
Contains the results from the dynbenchmark evaluation, see https://github.com/dynverse/dynbenchmark
2•6•0•0•Updated Oct 28, 2021Oct 28, 2021
proxyC
Public
R package for large-scale similarity/distance computation
R
•
GNU General Public License v3.0
•6•0•0•0•Updated Aug 31, 2021Aug 31, 2021
dyno
Public
Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
single-cell-omics visualisation trajectory trajectory-inference
R
•
Other
•32•170•64•0•Updated Jun 24, 2021Jun 24, 2021
dyngen_manuscript
Public
TeX
•0•6•2•0•Updated May 21, 2021May 21, 2021
dynsite
Public
Generator for the dynverse website at dynverse.github.io
HTML
•
Other
•0•0•0•0•Updated May 20, 2021May 20, 2021
dynverse.github.io
Public
Hub website for the dynverse, pointing visitors towards the different repositories and app
HTML
•0•0•0•0•Updated May 20, 2021May 20, 2021
dyncli
Public
CLI helper package for creating TI containers
R
•2•0•0•0•Updated May 20, 2021May 20, 2021
dynverse
Public
A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
scrna-seq single-cell single-cell-rna-seq single-cell-omics benchmarking trajectory-inference-methods
R
•
Other
•15•72•3•0•Updated May 20, 2021May 20, 2021
dyndimred
Public
Dimred methods for TI
R
•
Other
•2•7•1•0•Updated Mar 23, 2021Mar 23, 2021
dynparam
Public
R
•0•2•0•0•Updated Jan 4, 2021Jan 4, 2021
SingleCellOpenProblems
Public
Formalizing and benchmarking open problems in single-cell genomics
HTML
•
MIT License
•80•0•0•0•Updated Nov 24, 2020Nov 24, 2020
travis_package_cacher
Public
Helper repository to make daily caches of dynverse packages
Shell
•0•0•0•0•Updated Aug 26, 2020Aug 26, 2020
ti_forks
Public
Python
•
Other
•1•0•0•0•Updated Aug 24, 2020Aug 24, 2020
ti_cellrouter
Public
R
•
Other
•1•0•0•0•Updated Aug 24, 2020Aug 24, 2020
ti_paga
Public
Python
•
Other
•1•1•3•0•Updated Aug 21, 2020Aug 21, 2020
ti_monocle3
Public
R
•
Other
•1•0•1•1•Updated Aug 17, 2020Aug 17, 2020
ti_scorpius
Public
R
•
Other
•1•1•0•0•Updated Jul 13, 2020Jul 13, 2020