README.md

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A collection of 55 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 | Version | Build status | | | CALISTA | | code | Version | Build status | Nan Papili Gao | | CellRouter | | code | Version | Build status | Edroaldo Lummertz da Rocha James J. Collins George Q. Daley | | CellTrails | | code | Version | Build status | Daniel Ellwanger | | cellTree Gibbs | | code | Version | Build status | David duVerle Koji Tsuda | | cellTree maptpx | | code | Version | Build status | David duVerle Koji Tsuda | | cellTree vem | | code | Version | Build status | David duVerle Koji Tsuda | | Component 1 | | code | Version | Build status | | | DPT | | code | Version | Build status | Laleh HaghverdiPhilipp Angerer Fabian Theis | | ElPiGraph | | code | Version | Build status | Luca Albergante | | ElPiGraph - Cycle | | code | Version | Build status | Luca Albergante | | ElPiGraph - Linear | | code | Version | Build status | Luca Albergante | | Embeddr | | code | Version | Build status | Kieran Campbell | | FateID | | code | Version | Build status | Dominic Grün | | FORKS | | code | Version | Build status | Mayank Sharma | | GNG | | code | Version | Build status | Robrecht Cannoodt | | GPfates | | code | Version | Build status | Valentine Svensson Sarah A. Teichmann | | GrandPrix | | code | Version | Build status | Sumon Ahmed | | MATCHER | | code | Version | Build status | Joshua Welch Jan Prins | | MERLoT | | code | Version | Build status | Gonzalo Parra Johannes Söding | | MFA | | code | Version | Build status | Kieran Campbell Christopher Yau | | Monocle DDRTree | | code | Version | Build status | Xiaojie Qiu Cole Trapnell | | Monocle ICA | | code | Version | Build status | Xiaojie Qiu Cole Trapnell | | Mpath | | code | Version | Build status | Michael Poidinger Jinmiao Chen | | MST | | code | Version | Build status | | | ouija | | code | Version | Build status | Kieran Campbell Christopher Yau | | ouijaflow | | code | Version | Build status | Kieran Campbell Christopher Yau | | PAGA | | code | Version | Build status | Alexander Wolf Fabian Theis | | PAGA Tree | | code | Version | Build status | Alexander Wolf Fabian Theis | | pCreode | | code | Version | Build status | Charles A. Herring Ken S. Lau | | Periodic PrinCurve | | code | Version | Build status | | | PhenoPath | | code | Version | Build status | Kieran Campbell Christopher Yau | | Projected DPT | | code | Version | Build status | | | Projected Monocle | | code | Version | Build status | | | Projected PAGA | | code | Version | Build status | | | Projected Slingshot | | code | Version | Build status | | | Projected TSCAN | | code | Version | Build status | | | pseudogp | | code | Version | Build status | Kieran Campbell Christopher Yau | | RaceID / StemID | | code | Version | Build status | Dominic Grün Alexander van Oudenaarden | | reCAT | | code | Version | Build status | Riu Jian | | SCIMITAR | | code | Version | Build status | Josh Stuart | | SCORPIUS | | code | Version | Build status | Robrecht Cannoodt Wouter Saelens Yvan Saeys | | SCOUP | | code | Version | Build status | Hirotaka Matsumoto | | SCUBA | | code | Version | Build status | Eugenio Marco Gregory Giecold Guo-Cheng Yuan | | Sincell | | code | Version | Build status | Antonio Rausell Miguel Julia | | SLICE | | code | Version | Build status | Yan Xu Minzhe Guo | | SLICER | | code | Version | Build status | Joshua Welch Jan Prins | | Slingshot | | code | Version | Build status | Kelly Street Sandrine Dudoit | | STEMNET | | code | Version | Build status | Lars Velten | | topslam | | code | Version | Build status | Max Zwiessele | | TSCAN | | code | Version | Build status | Zhicheng Ji Hongkai Ji | | URD | | code | Version | Build status | Jeffrey A. Farrell | | Wanderlust | | code | Version | Build status | Manu Setty Dana Pe’er | | Waterfall | | code | Version | Build status | Jaehoon ShinHongjun Song | | Wishbone | | code | Version | Build status | Manu Setty Dana Pe’er |

Sources

We used following resources to get a (hopefully exhaustive) list of all TI methods:

Anthony Gitter’s single-cell-pseudotime DOI

Sean Davis’ awesome-single-cell DOI

Luke Zappia’s scRNA-tools DOI

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)

Recent changes in dynmethods 1.0.5 (03-07-2019)

Dynverse dependencies



dynverse/dynmethods documentation built on July 6, 2019, 11:30 a.m.