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<br><img src="man/figures/logo.png" align="right" /> # A collection of 56 trajectory inference methods This package contains wrappers for trajectory inference (TI) methods. The output of each method is transformed into a common trajectory model using dynwrap, which allows easy visualisation and comparison. All methods are wrapped inside a docker container, which avoids dependency issues, and also makes it easy to add a new method.
To run any of these methods, interpret the results and visualise the trajectory, see the dyno package.
To include your own method, feel free to send us a pull request or create an issue. The easiest way to add a new method is through a docker container, so that dependencies don’t pose any issues for other users, but we also welcome methods directly wrapped inside of R. The main benefit of adding your own method is that users can easily compare your method with others and visualise/interpret the output. Moreover, your method will be compared to other methods within the TI method evaluation.
List of included methods
| Method | Doi | Code | Docker | Status | Authors |
|---|---|---|---|---|---|
| Angle | code |  |  | ||
| CALISTA | <a href='https://doi.org/10.1101/257550'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Nan Papili Gao <a href='https://github.com/nanp'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| CellRouter | <a href='https://doi.org/10.1038/s41467-018-03214-y'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Edroaldo Lummertz da Rocha <a href='https://orcid.org/0000-0003-0537-4223'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/edroaldo'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>James J. Collins <a href='https://orcid.org/0000-0003-0537-4223'><img src='man/figures/orcid_logo.svg' height='16'></a></sub><br><sub>George Q. Daley</sub> |
| CellTrails | <a href='https://doi.org/10.1016/j.celrep.2018.05.002'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Daniel Ellwanger <a href='https://github.com/dcellwanger'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| Component 1 | code |  |  | ||
| DPT | <a href='https://doi.org/10.1038/nmeth.3971'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Laleh Haghverdi</sub><br><sub>Philipp Angerer <a href='https://orcid.org/0000-0002-0369-2888'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/flying-sheep'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Fabian Theis <a href='https://orcid.org/0000-0002-2419-1943'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/theislab'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| ElPiGraph | code |  |  | <sub>Luca Albergante <a href='https://orcid.org/0000-0001-8151-6989'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/Albluca'><img src='man/figures/github_logo.png' height='16'></a></sub> | |
| ElPiGraph - Cycle | code |  |  | <sub>Luca Albergante <a href='https://orcid.org/0000-0001-8151-6989'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/Albluca'><img src='man/figures/github_logo.png' height='16'></a></sub> | |
| ElPiGraph - Linear | code |  |  | <sub>Luca Albergante <a href='https://orcid.org/0000-0001-8151-6989'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/Albluca'><img src='man/figures/github_logo.png' height='16'></a></sub> | |
| Embeddr | <a href='https://doi.org/10.1101/027219'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Kieran Campbell <a href='https://github.com/kieranrcampbell'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| FORKS | <a href='https://doi.org/10.1101/132811'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Mayank Sharma <a href='https://github.com/macsharma'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| FateID | <a href='https://doi.org/10.1038/nmeth.4662'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Dominic Grün <a href='https://github.com/dgrun'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| GNG | code |  |  | <sub>Robrecht Cannoodt <a href='https://orcid.org/0000-0003-3641-729X'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/rcannood'><img src='man/figures/github_logo.png' height='16'></a></sub> | |
| GPfates | <a href='https://doi.org/10.1126/sciimmunol.aal2192'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Valentine Svensson <a href='https://orcid.org/0000-0002-9217-2330'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/vals'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Sarah A. Teichmann <a href='https://orcid.org/0000-0002-6294-6366'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/Teichlab'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| GrandPrix | <a href='https://doi.org/10.1101/227843'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Sumon Ahmed <a href='https://github.com/sumonahmedUoM'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| MATCHER | <a href='https://doi.org/10.1186/s13059-017-1269-0'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Joshua Welch <a href='https://github.com/jw156605'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Jan Prins</sub> |
| MERLoT | <a href='https://doi.org/10.1101/261768'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Gonzalo Parra <a href='https://orcid.org/0000-0003-2446-016X'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/gonzaparra'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Johannes Söding <a href='https://orcid.org/0000-0001-9642-8244'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/soedinglab'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| MFA | <a href='https://doi.org/10.12688/wellcomeopenres.11087.1'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Kieran Campbell <a href='https://github.com/kieranrcampbell'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Christopher Yau <a href='https://orcid.org/0000-0001-7615-8523'><img src='man/figures/orcid_logo.svg' height='16'></a></sub> |
| MST | code |  |  | ||
| Monocle DDRTree | <a href='https://doi.org/10.1038/nmeth.4402'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Xiaojie Qiu <a href='https://github.com/Xiaojieqiu'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Cole Trapnell <a href='https://orcid.org/0000-0002-8105-4347'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/ctrapnell'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| Monocle ICA | <a href='https://doi.org/10.1038/nmeth.4402'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Xiaojie Qiu <a href='https://github.com/Xiaojieqiu'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Cole Trapnell <a href='https://orcid.org/0000-0002-8105-4347'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/ctrapnell'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| Mpath | <a href='https://doi.org/10.1038/ncomms11988'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Michael Poidinger <a href='https://orcid.org/0000-0002-1047-2277'><img src='man/figures/orcid_logo.svg' height='16'></a></sub><br><sub>Jinmiao Chen <a href='https://orcid.org/0000-0001-7547-6423'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/jinmiaochen'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| Oscope | <a href='https://doi.org/10.1038/nmeth.3549'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Ning Leng <a href='https://orcid.org/0000-0003-3641-729X'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/lengning'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| PAGA | <a href='https://doi.org/10.1186/s13059-019-1663-x'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Alexander Wolf <a href='https://orcid.org/0000-0002-8760-7838'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/falexwolf'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Fabian Theis <a href='https://github.com/theislab'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| PAGA Tree | <a href='https://doi.org/10.1186/s13059-019-1663-x'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Alexander Wolf <a href='https://orcid.org/0000-0002-8760-7838'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/falexwolf'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Fabian Theis <a href='https://github.com/theislab'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| Periodic PrinCurve | code |  |  | ||
| PhenoPath | <a href='https://doi.org/10.1101/159913'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Kieran Campbell <a href='https://github.com/kieranrcampbell'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Christopher Yau <a href='https://orcid.org/0000-0001-7615-8523'><img src='man/figures/orcid_logo.svg' height='16'></a></sub> |
| Projected DPT | code |  |  | ||
| Projected Monocle | code |  |  | ||
| Projected PAGA | <a href='https://doi.org/10.1101/208819'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | |
| Projected Slingshot | <a href='https://doi.org/10.1186/s12864-018-4772-0'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | |
| Projected TSCAN | code |  |  | ||
| RaceID / StemID | <a href='https://doi.org/10.1016/j.stem.2016.05.010'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Dominic Grün <a href='https://github.com/dgrun'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Alexander van Oudenaarden <a href='https://github.com/avolab'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| SCIMITAR | <a href='https://doi.org/10.1142/9789813207813_0053'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Josh Stuart <a href='https://github.com/dimenwarper'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| SCORPIUS | <a href='https://doi.org/10.1101/079509'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Robrecht Cannoodt <a href='https://orcid.org/0000-0003-3641-729X'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/rcannood'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Wouter Saelens <a href='https://orcid.org/0000-0002-7114-6248'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/zouter'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Yvan Saeys <a href='https://github.com/saeyslab'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| SCOUP | <a href='https://doi.org/10.1186/s12859-016-1109-3'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Hirotaka Matsumoto <a href='https://github.com/hmatsu1226'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| SCUBA | <a href='https://doi.org/10.1073/pnas.1408993111'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Eugenio Marco <a href='https://github.com/eugeniomarco'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Gregory Giecold <a href='https://github.com/GGiecold'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Guo-Cheng Yuan <a href='https://orcid.org/0000-0002-2283-4714'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/gcyuan'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| SLICE | <a href='https://doi.org/10.1093/nar/gkw1278'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Yan Xu <a href='https://github.com/xu-lab'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Minzhe Guo <a href='https://github.com/minzheguo'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| SLICER | <a href='https://doi.org/10.1186/s13059-016-0975-3'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Joshua Welch <a href='https://github.com/jw156605'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Jan Prins</sub> |
| STEMNET | <a href='https://doi.org/10.1038/ncb3493'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Lars Velten <a href='https://orcid.org/0000-0002-1233-5874'><img src='man/figures/orcid_logo.svg' height='16'></a></sub> |
| Sincell | <a href='https://doi.org/10.1093/bioinformatics/btv368'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Antonio Rausell <a href='https://github.com/Cortalak'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Miguel Julia</sub> |
| Slingshot | <a href='https://doi.org/10.1186/s12864-018-4772-0'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Kelly Street <a href='https://github.com/kstreet13'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Sandrine Dudoit <a href='https://orcid.org/0000-0002-6069-8629'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/sandrinedudoit'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| TSCAN | <a href='https://doi.org/10.1093/nar/gkw430'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Zhicheng Ji <a href='https://github.com/zji90'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Hongkai Ji</sub> |
| URD | <a href='https://doi.org/10.1126/science.aar3131'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Jeffrey A. Farrell <a href='https://github.com/farrellja'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| Wanderlust | <a href='https://doi.org/10.1016/j.cell.2014.04.005'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Manu Setty <a href='https://github.com/ManuSetty'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Dana Pe’er <a href='https://orcid.org/0000-0002-9259-8817'><img src='man/figures/orcid_logo.svg' height='16'></a></sub> |
| Waterfall | <a href='https://doi.org/10.1016/j.stem.2015.07.013'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Jaehoon Shin</sub><br><sub>Hongjun Song</sub> |
| Wishbone | <a href='https://doi.org/10.1038/nbt.3569'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Manu Setty <a href='https://github.com/ManuSetty'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Dana Pe’er <a href='https://orcid.org/0000-0002-9259-8817'><img src='man/figures/orcid_logo.svg' height='16'></a></sub> |
| cellTree Gibbs | <a href='https://doi.org/10.1186/s12859-016-1175-6'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>David duVerle <a href='https://orcid.org/0000-0003-2836-0502'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/david-duverle'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Koji Tsuda <a href='https://orcid.org/0000-0002-4288-1606'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/tsudalab'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| cellTree maptpx | <a href='https://doi.org/10.1186/s12859-016-1175-6'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>David duVerle <a href='https://orcid.org/0000-0003-2836-0502'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/david-duverle'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Koji Tsuda <a href='https://orcid.org/0000-0002-4288-1606'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/tsudalab'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| cellTree vem | <a href='https://doi.org/10.1186/s12859-016-1175-6'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>David duVerle <a href='https://orcid.org/0000-0003-2836-0502'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/david-duverle'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Koji Tsuda <a href='https://orcid.org/0000-0002-4288-1606'><img src='man/figures/orcid_logo.svg' height='16'></a> <a href='https://github.com/tsudalab'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| ouija | <a href='https://doi.org/10.1101/060442'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Kieran Campbell <a href='https://github.com/kieranrcampbell'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Christopher Yau <a href='https://orcid.org/0000-0001-7615-8523'><img src='man/figures/orcid_logo.svg' height='16'></a></sub> |
| ouijaflow | <a href='https://doi.org/10.1101/060442'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Kieran Campbell <a href='https://github.com/kieranrcampbell'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Christopher Yau</sub> |
| pCreode | <a href='https://doi.org/10.1016/j.cels.2017.10.012'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Charles A. Herring <a href='https://github.com/herrinca'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Ken S. Lau <a href='https://github.com/KenLauLab'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| pseudogp | <a href='https://doi.org/10.1371/journal.pcbi.1005212'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Kieran Campbell <a href='https://github.com/kieranrcampbell'><img src='man/figures/github_logo.png' height='16'></a></sub><br><sub>Christopher Yau <a href='https://orcid.org/0000-0001-7615-8523'><img src='man/figures/orcid_logo.svg' height='16'></a></sub> |
| reCAT | <a href='https://doi.org/10.1038/s41467-017-00039-z'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Riu Jian <a href='https://github.com/louhzmaki'><img src='man/figures/github_logo.png' height='16'></a></sub> |
| topslam | <a href='https://doi.org/10.1101/057778'><img src='man/figures/doi_logo.png' height='16'></a> | code |  |  | <sub>Max Zwiessele <a href='https://github.com/mzwiessele'><img src='man/figures/github_logo.png' height='16'></a></sub> |
Sources
We used following resources to get a (hopefully exhaustive) list of all TI methods:
Anthony Gitter’s
single-cell-pseudotime
Sean Davis’
awesome-single-cell
New methods
Some methods are not wrapped (yet). Check out the issues for an overview
Latest changes
Check out news(package = "dynwrap") or NEWS.md for a full
list of changes.
Recent changes in dynmethods 1.1.0 (unreleased)
-
MAJOR CHANGE: Add functionality to switch between R wrappers and container wrappers.
-
MAJOR CHANGE: Add R wrappers for SCORPIUS.
-
BUG FIX: Do not install R packages if version is not specified and package is installed.
Recent changes in dynmethods 1.0.5 (03-07-2019)
- SMALL CHANGES: Updates for scorpius, slingshot, paga, paga_tree and paga_projected
Dynverse dependencies
<!-- Generated by "update_dependency_graphs.R" in the main dynverse repo -->