A collection of 57 trajectory inference methods

This package contains wrappers for all of the trajectory inference (TI) methods included in the dynverse review. The output of each method is transformed into a common trajectory model using dynwrap, which allows easy visualisation and comparison. Nearly all methods are integrated within a docker container, avoiding dependency issues. Some methods are also directly wrapped inside of R.

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.

All methods are automatically tested on our cluster on some small toy and real datasets. Results of the automated testing

List of included methods

Method		Authors
CALISTA	✓ (code, dockerhub)	_{Nan Papili Gao}
CellRouter	✓ (code, dockerhub)	_{Edroaldo Lummertz da Rocha} _{James J. Collins} _{George Q. Daley}
CellTrails	✓ (code, dockerhub)	_{Daniel Ellwanger}
cellTree with gibbs	✓ (code, dockerhub)	_{David duVerle} _{Koji Tsuda}
cellTree with maptpx	✓ (code, dockerhub)	_{David duVerle} _{Koji Tsuda}
cellTree with vem	✓ (code, dockerhub)	_{David duVerle} _{Koji Tsuda}
DPT	✓ (code, dockerhub)	_{Laleh Haghverdi} _{Philipp Angerer} _{Fabian Theis}
ElPiGraph	✓ (code, dockerhub)	_{Luca Albergante}
ElPiGraph cycle	✓ (code, dockerhub)	_{Luca Albergante}
ElPiGraph linear	✓ (code, dockerhub)	_{Luca Albergante}
Embeddr	✓ (code, dockerhub)	_{Kieran Campbell}
FateID	✓ (code, dockerhub)	_{Dominic Grün}
FORKS	✓ (code, dockerhub)	_{Mayank Sharma}
GPfates	✓ (code, dockerhub)	_{Valentine Svensson} _{Sarah A. Teichmann}
GrandPrix	✓ (code, dockerhub)	_{Sumon Ahmed}
MATCHER	✓ (code, dockerhub)	_{Joshua Welch} _{Jan Prins}
MERLoT	✓ (code, dockerhub)	_{Gonzalo Parra} _{Johannes Söding}
mfa	✓ (code, dockerhub)	_{Kieran Campbell} _{Christopher Yau}
Monocle DDRTree	✓ (code, dockerhub)	_{Xiaojie Qiu} _{Cole Trapnell}
Monocle ICA	✓ (code, dockerhub)	_{Xiaojie Qiu} _{Cole Trapnell}
Mpath	✓ (code, dockerhub)	_{Michael Poidinger} _{Jinmiao Chen}
ouija	✓ (code, dockerhub)	_{Kieran Campbell} _{Christopher Yau}
ouijaflow	✓ (code, dockerhub)	_{Kieran Campbell} _{Christopher Yau}
PAGA	✓ (code, dockerhub)	_{Alexander Wolf} _{Fabian Theis}
pCreode	✓ (code, dockerhub)	_{Charles A. Herring} _{Ken S. Lau}
PhenoPath	✓ (code, dockerhub)	_{Kieran Campbell} _{Christopher Yau}
pseudogp	✓ (code, dockerhub)	_{Kieran Campbell} _{Christopher Yau}
RaceID / StemID	✓ (code, dockerhub)	_{Dominic Grün} _{Alexander van Oudenaarden}
reCAT	✓ (code, dockerhub)	_{Riu Jian}
SCIMITAR	✓ (code, dockerhub)	_{Josh Stuart}
SCORPIUS	✓ (code, dockerhub)	_{Robrecht Cannoodt} _{Wouter Saelens} _{Yvan Saeys}
SCOUP	✓ (code, dockerhub)	_{Hirotaka Matsumoto}
SCUBA	✓ (code, dockerhub)	_{Eugenio Marco} _{Gregory Giecold} _{Guo-Cheng Yuan}
Sincell	✓ (code, dockerhub)	_{Antonio Rausell} _{Miguel Julia}
SLICE	✓ (code, dockerhub)	_{Yan Xu} _{Minzhe Guo}
SLICER	✓ (code, dockerhub)	_{Joshua Welch} _{Jan Prins}
Slingshot	✓ (code, dockerhub)	_{Kelly Street} _{Sandrine Dudoit}
STEMNET	✓ (code, dockerhub)	_{Lars Velten}
topslam	✓ (code, dockerhub)	_{Max Zwiessele}
TSCAN	✓ (code, dockerhub)	_{Zhicheng Ji} _{Hongkai Ji}
URD	✓ (code, dockerhub)	_{Jeffrey A. Farrell}
Wanderlust	✓ (code, dockerhub)	_{Manu Setty} _{Dana Pe'er}
Waterfall	✓ (code, dockerhub)	_{Jaehoon Shin} _{Hongjun Song}
Wishbone	✓ (code, dockerhub)	_{Manu Setty} _{Dana Pe'er}
Periodic PrinCurve	✓ (code, dockerhub)	_{Robrecht Cannoodt} _{Wouter Saelens}
Projected DPT	✓ (code, dockerhub)
Projected GNG	✓ (code, dockerhub)	_{Robrecht Cannoodt}
Projected Monocle	✓ (code, dockerhub)
Projected PAGA	✓ (code, dockerhub)
Projected Slingshot	✓ (code, dockerhub)
Projected TSCAN	✓ (code, dockerhub)
Angle	✓ (code, dockerhub)	_{Robrecht Cannoodt} _{Wouter Saelens}
Component 1	✓ (code, dockerhub)
Control: error	✓ (code, dockerhub)	_{Robrecht Cannoodt} _{Wouter Saelens}
Control: random	✓ (code, dockerhub)	_{Robrecht Cannoodt} _{Wouter Saelens}
Control: identity	✓ (code, dockerhub)	_{Robrecht Cannoodt} _{Wouter Saelens}
Control: shuffle	✓ (code, dockerhub)	_{Robrecht Cannoodt} _{Wouter Saelens}