{"Package":"dynwrap","Type":"Package","Title":"Representing and Inferring Single-Cell Trajectories","Description":"Provides functionality to infer trajectories from single-cell data,\nrepresent them into a common format, and adapt them. Other biological information\ncan also be added, such as cellular grouping, RNA velocity and annotation.\nSaelens et al. (2019) .","Version":"1.2.2","Authors@R":"c(\nperson(\n\"Robrecht\",\n\"Cannoodt\",\nemail = \"rcannood@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3641-729X\", github = \"rcannood\")\n),\nperson(\n\"Wouter\",\n\"Saelens\",\nemail = \"wouter.saelens@gmail.com\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-7114-6248\", github = \"zouter\")\n)\n)","URL":"https://github.com/dynverse/dynwrap","BugReports":"https://github.com/dynverse/dynwrap/issues","License":"MIT + file LICENSE","LazyData":"TRUE","RoxygenNote":"7.1.1","Encoding":"UTF-8","Depends":"R (>= 3.0.0)","Imports":"assertthat, babelwhale, crayon, dplyr, dynutils (>= 1.0.3),\ndynparam, igraph, glue, magrittr, Matrix, methods, purrr,\nprocessx, readr, stringr, reshape2, tibble, tidyr, yaml","Suggests":"dyndimred, hdf5r, knitr, pkgload, ranger, rmarkdown, testthat","VignetteBuilder":"knitr","NeedsCompilation":"no","Packaged":"2021-03-23 22:05:51 UTC; rcannood","Author":"Robrecht Cannoodt [aut, cre] (,\nrcannood),\nWouter Saelens [aut] (, zouter)","Maintainer":"Robrecht Cannoodt ","Repository":"CRAN","Date/Publication":"2021-03-23 22:40:02 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/dynwrap_1.2.2.tar.gz","jsonAuthors":[{"name":"Robrecht Cannoodt","email":"rcannood@gmail.com","maintainer":true},{"name":"Wouter Saelens","email":"wouter.saelens@gmail.com","maintainer":false}],"readme":"dynwrap: Representing and Inferring Single-Cell Trajectories\n================\n\n\n\n[![R-CMD-check](https://github.com/dynverse/dynwrap/workflows/R-CMD-check/badge.svg)](https://github.com/dynverse/dynwrap/actions?query=workflow%3AR-CMD-check)\n[![codecov](https://codecov.io/gh/dynverse/dynwrap/branch/master/graph/badge.svg)](https://codecov.io/gh/dynverse/dynwrap)\n[**ℹ️ Tutorials**](https://dynverse.org) [**ℹ️ Reference\ndocumentation**](https://dynverse.org/reference/dynwrap/)
\n

\n\n**dynwrap** contains the code for a common model of single-cell\ntrajectories. The package can:\n\n- Wrap the input data of a trajectory inference method, such as\n expression and prior information\n- Run a trajectory inference method in R, in a docker container or a\n singularity container\n- Wrap the output of a trajectory inference method, such as the\n pseudotime, a clustering or a branch network, and convert it into a\n common trajectory model\n- Further postprocess and adapt the trajectory model, such as\n labelling the milestones and rooting the trajectory\n\n![](man/figures/trajectory_model.png)\n\nDocumentation and the API reference for dynwrap can be found at the\ndyvnerse documentation website: .\n\ndynwrap was used to wrap 50+ trajectory inference method within docker\ncontainers in [dynmethods](https://github.com/dynverse/dynmethods).\n\n![](man/figures/overview_wrapping_v3.png)\n\nThe advantage of using a common model is that it allows:\n\n- Comparison between a prediction and a gold standard, eg. using\n [dyneval](https://github.com/dynverse/dyneval)\n- Comparing two predictions\n- Easily visualise the trajectory, eg. using\n [dynplot](https://github.com/dynverse/dynplot)\n- Extracting relevant features/genes, eg. using\n [dynfeature](https://github.com/dynverse/dynfeature)\n\n## Latest changes\n\nCheck out `news(package = \"dynwrap\")` or [NEWS.md](NEWS.md) for a full\nlist of changes.\n\n\n\n### Recent changes in dynwrap 1.2.2\n\n- MAJOR CHANGE `convert_milestone_percentages_to_progressions()`:\n Rewrite implementation to attain significant speedup.\n\n- MINOR CHANGE `infer_trajectory()`: Infer command (Rscript/python)\n from file extension if possible and avoid using shebang to execute\n script, because R CMD check for R 4.0 puts Rscript and R dummy\n executables on the path before R CMD check. This means\n `#!/usr/bin/env Rscript` does not work anymore.\n\n- MINOR CHANGE `add_feature_importance()`: Add a function for adding\n feature importance scores to a trajectory.\n\n- BUG FIX `project_waypoints()`: Rename milestone waypoints such that\n the names are unique.\n\n- BUG FIX `infer_trajectory()`: Fix error message printing.\n\n- BUG FIX: `dyndimred` is used conditionally.\n\n- BUG FIX: `wrap_expression()` and `add_expression()`: Do not override\n feature\\_info when it already exists in dataset.\n\n### Recent changes in dynwrap 1.2.1 (2020-05-11)\n\n- BUG FIX `project_trajectory()`: Correctly pass parameters.\n\n- MINOR CHANGES `select_waypoints()`: Do not recompute waypoints if\n trajectory already contains some.\n\n- MINOR CHANGES `convert_progressions_to_milestone_percentages()`:\n Solve tapply issues ahead of dplyr 1.0 release.\n\n## Dynverse dependencies\n\n\n\n![](man/figures/dependencies.png)","jobInfo":{"package":"dynwrap","version":"1.2.2","parsingStatus":"success","parserVersion":2,"parsedAt":"2023-03-01T18:29:48+0000"}}

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