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dynwrap 1.2.4

• Resubmission after babelwhale was removed from CRAN.

• MINOR CHANGE: Added @return documentation to all functions.

dynwrap 1.2.3

• MINOR CHANGE: Fixes to metadata (documentation, citation entry, broken links).

• MINOR CHANGE: Use alternative method for checking whether dynmethods is installed.

dynwrap 1.2.2

• MAJOR CHANGE convert_milestone_percentages_to_progressions(): Rewrite implementation to attain significant speedup.

• MINOR CHANGE infer_trajectory(): Infer command (Rscript/python) from file extension if possible and avoid using shebang to execute script, because R CMD check for R 4.0 puts Rscript and R dummy executables on the path before R CMD check. This means #!/usr/bin/env Rscript does not work anymore.

• MINOR CHANGE add_feature_importance(): Add a function for adding feature importance scores to a trajectory.

• BUG FIX project_waypoints(): Rename milestone waypoints such that the names are unique.

• BUG FIX infer_trajectory(): Fix error message printing.

• BUG FIX: dyndimred is used conditionally.

• BUG FIX: wrap_expression() and add_expression(): Do not override feature_info when it already exists in dataset.

dynwrap 1.2.1 (2020-05-11)

• BUG FIX project_trajectory(): Correctly pass parameters.

• MINOR CHANGES select_waypoints(): Do not recompute waypoints if trajectory already contains some.

• MINOR CHANGES convert_progressions_to_milestone_percentages(): Solve tapply issues ahead of dplyr 1.0 release.

dynwrap 1.2.0 (2020-03-09)

• FUNCTIONALITY: Improved RNA velocity handling. Not all features need to be present in the projected expression, allowing integration with standard velocyto.R pipelines.

• BUG FIX calculate_pseudotime(): Fix pseudotime calculation on branching trajectories (#139).

• BUG FIX flip_edges(): Also flip dimred_segment_progressions if available.

• BUG FIX add_root(): Fix rooting for some linear trajectories (#149)

• MINOR CHANGES: Allow a named vector for groups_id prior information (#154)

• MINOR CHANGES: Moved orient_topology_to_velocity() to scvelo R package.

• BUG FIX simplify_trajectory(): handle dimred_milestones and dimred_segments values (#153).

• BUG FIX add_dimred(): Do not execute example of dyndimred if is not installed.

dynwrap 1.1.4 (11-10-2019)

First CRAN release!

• BUG FIX: Fixed #142 where the error message was truncated

• DOCUMENTATION: Added examples to all functions.

dynwrap 1.1.3 (05-06-2019)

• MINOR CHANGE add_dimred(): Add a separate argument for specifying the projected dimred rather than expecting the projected dimred to be passed as additional columns in dimred.

• BUG FIX: Fix for dynverse/dyno#52, do specify whether or not to use optional priors when passed.

dynwrap 1.1.2 (08-05-2019)

• FEATURE: Add leaves_n as prior information

dynwrap 1.1.1 (08-05-2019)

• BUG FIX: Fixed bug for directed geodesic distances with disconnected gra phs, dynverse/dynplot#37

dynwrap 1.1 (07-05-2019)

• FEATURE: RNA velocity data can now be included in the wrapper

• FEATURE: RNA velocity projected expression can now be given to methods

• FEATURE: Added orient_topology_to_velocity() to orient the edges of a trajectory based on the velocity vectors

• FEATURE: calculate_geodesic_distances() now has a directed parameter, with which you can calculate directed geodesic distances. Unreachable cells will receive an infinite distance

• FEATURE: Added projected_trajectory() (ported from dynplot). add_dimred() will now by default also add a projection of the trajectory to the data

dynwrap 1.0.1 (09-04-2019)

• MINOR CHANGE: infer_trajectory(..., debug = TRUE) will now return commands for both entering the container and running the dyncli::main() function inside the container

• MINOR CHANGE: Make create_ti_method_definition() actually work

• DOCUMENTATION: Added examples for each trajectory wrapper

• DOCUMENTATION: Added vignette discussing wrapper types

• DOCUMENTATION: Added vignette discussing create_ti_method_definition()

• BUG FIX: Fixed bug where sink() was not removed after interruption

dynwrap 1.0.0 (28-03-2019)

• MAJOR CHANGE: Add support for Singularity 3.0, drop support for previous releases of Singularity and singularity-hub.

• MAJOR CHANGE: dynwrap now always works with sparse count and expression matrices

• FEATURE: Add create_ti_method_definition() to create a definition from a local script.

• DOCUMENTATION: Major update of all documentation for dynbenchmark publication

• MINOR CHANGE: Rename compute_tented_geodesic_distances() to calculate_geodesic_distances()

• MINOR CHANGE: Harmonisation of function arguments to either dataset or trajectory

dynwrap 0.3.1.2 (01-02-2019)

• BUG FIX: simplify_replace_edges() would sometimes swap edges in milestone network around, but forget invert percentages.

• BUG FIX: Close sinks when interupting the R process

• MINOR CHANGE: Work with new babelwhale, which includes support for singularity 3.0

dynwrap 0.3.1.1 (17-12-2018)

• CLEAN UP: Removed helper functions that are not required any more: get_env_or_null(), read_rds_or_null() and print_processx().

• MINOR CHANGE: remove requirement that milestone_ids and cell_ids cannot overlap

dynwrap 0.3.1 (19-11-2018)

• HOTFIX: Use utils::data() to get access to priors.

dynwrap 0.3.0 (19-11-2018)

• MINOR CHANGE: Added metadata on the different wrapper types implemented in dynwrap.

• CLEAN UP: Removed plot_fun argument from create_ti_method().

• MINOR CHANGE: Replaced mc_cores with more flexible map_fun.

• MINOR CHANGE: Renamed create_ti_method() to create_ti_method_r(), and create_ti_method_with_container() to create_ti_method_container().

• CLEAN UP: Drastically reworked create_ti_method_r() and create_ti_method_container(), and the underlying functions for executing a method on a dataset.

• CLEAN UP: Remove parse_parameter_definition() and thereby dependency on ParamHelpers.

dynwrap 0.2.0 (29-10-2018)

• BUG FIX: Fixed incorrect calculation of milestone percentage during trajectory simplification. Occurs only in a rare edge case, namely when the order of the milestones in the milestone network is very different from the order of the milestone ids (0475e94).

• BUG FIX: Fixed suggested dependencies not being installed in the dynwrap containers (#100).

• FEATURE REMOVAL: Removed feather data format because it’s not being used and creates dependency issues every now and again.

• BUG FIX: devtools:::shim_system.file() has been moved to pkgload:::shim_system.file().

• TESTING: Solved issue with the unit tests by not using any helpers.

• MINOR CHANGE: Have docker images build from dynwrap@devel.

• BUG FIX: Remove option(echo = FALSE) from .Rprofile in recipes because some packages directly rely on standard output from R, so printing the command wreaks havoc.

dynwrap 0.1.0 (07-03-2018)

• INITIAL RELEASE: dynwrap, functionality for containerised trajectory inference.
• Wrap the input data of a trajectory inference method, such as expression and prior information
• Run a trajectory inference method in R, in a docker container or a singularity container
• Wrap the output of a trajectory inference method, such as the pseudotime, a clustering or a branch network, and convert it into a common trajectory model
• Further postprocess the trajectory model, such as labelling the milestones and rooting the trajectory

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.