ℹ️ Tutorials ℹ️ Reference documentation

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	Code	Authors
Angle	code
CALISTA	code	_{Nan Papili Gao}
CellRouter	code	_{Edroaldo Lummertz da Rocha} _{James J. Collins} _{George Q. Daley}
CellTrails	code	_{Daniel Ellwanger}
cellTree Gibbs	code	_{David duVerle} _{Koji Tsuda}
cellTree maptpx	code	_{David duVerle} _{Koji Tsuda}
cellTree vem	code	_{David duVerle} _{Koji Tsuda}
Component 1	code
DPT	code	_{Laleh Haghverdi} _{Philipp Angerer} _{Fabian Theis}
ElPiGraph	code	_{Luca Albergante}
ElPiGraph - Cycle	code	_{Luca Albergante}
ElPiGraph - Linear	code	_{Luca Albergante}
Embeddr	code	_{Kieran Campbell}
FateID	code	_{Dominic Grün}
FORKS	code	_{Mayank Sharma}
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}
Monocle DDRTree	code	_{Xiaojie Qiu} _{Cole Trapnell}
Monocle ICA	code	_{Xiaojie Qiu} _{Cole Trapnell}
Mpath	code	_{Michael Poidinger} _{Jinmiao Chen}
MST	code
ouija	code	_{Kieran Campbell} _{Christopher Yau}
ouijaflow	code	_{Kieran Campbell} _{Christopher Yau}
PAGA	code	_{Alexander Wolf} _{Fabian Theis}
PAGA Tree	code	_{Alexander Wolf} _{Fabian Theis}
pCreode	code	_{Charles A. Herring} _{Ken S. Lau}
Periodic PrinCurve	code
PhenoPath	code	_{Kieran Campbell} _{Christopher Yau}
Projected DPT	code
Projected Monocle	code
Projected PAGA	code
Projected Slingshot	code
Projected TSCAN	code
pseudogp	code	_{Kieran Campbell} _{Christopher Yau}
RaceID / StemID	code	_{Dominic Grün} _{Alexander van Oudenaarden}
reCAT	code	_{Riu Jian}
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}
Sincell	code	_{Antonio Rausell} _{Miguel Julia}
SLICE	code	_{Yan Xu} _{Minzhe Guo}
SLICER	code	_{Joshua Welch} _{Jan Prins}
Slingshot	code	_{Kelly Street} _{Sandrine Dudoit}
STEMNET	code	_{Lars Velten}
topslam	code	_{Max Zwiessele}
TSCAN	code	_{Zhicheng Ji} _{Hongkai Ji}
URD	code	_{Jeffrey A. Farrell}
Wanderlust	code	_{Manu Setty} _{Dana Pe’er}
Waterfall	code	_{Jaehoon Shin} _{Hongjun Song}
Wishbone	code	_{Manu Setty} _{Dana Pe’er}