README.md

In dynverse/dynmethods: A collection of trajectory inference methods

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

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

Luke Zappia’s scRNA-tools

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

dynverse/dynmethods documentation built on Jan. 18, 2024, 4:44 a.m.