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dyngen 1.0.0#27

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rcannood merged 152 commits intomasterdynverse/dyngen:masterfrom develdynverse/dyngen:develCopy head branch name to clipboardFeb 23, 2021

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Commits

Commits on Jul 17, 2020

• add cran comments

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Commits on Aug 8, 2020

• use quotes

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• add copyright holders

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Commits on Aug 17, 2020

• add examples

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Commits on Aug 24, 2020

• use donttest instead of dontrun

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• update cran comments

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Commits on Aug 26, 2020

• substitute dontrun with donttest

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Commits on Sep 2, 2020

• Added \value tags to exported functions.

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Commits on Sep 14, 2020

• wrap_dataset(): Fix drop = FALSE bug when only cell is being sampled.

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• reduce donttest time using dontshow

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• update readme

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Commits on Sep 15, 2020

• update vignette

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Commits on Sep 18, 2020

• update doi badge

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• Merge branch 'devel' of github.com:dynverse/dyngen into devel

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Commits on Oct 12, 2020

• set up weekly builds

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• allow simulating the targets in the gold standard simulation

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Commits on Jan 11, 2021

• allow to save platform-specific defaults for num_cores and download_cache_dir

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• fix namespace

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Commits on Jan 15, 2021

• Fix dockerfile

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• fix github action

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• make test smaller

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• rename wrap_dataset to as_dyno

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• add anndata conversion function

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Commits on Jan 18, 2021

• update vignettes

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• update news & vignettes

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• regenerate vignettes

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• split up the extract_parameters function

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• move combine function from dyngen.manuscript to dyngen

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• add vignette on simulating batch effects

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• add tests for combine models

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• fix errors & warnings

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• add WIP vignette for simulating knockouts

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• make the gold standard edge dotted

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• Extend documentation of KO vignette

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• remove :

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• should remove spaces

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• import aes_string

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Commits on Jan 19, 2021

• fix another import

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• update news and vignette

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Commits on Jan 20, 2021

• improve vignette

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Commits on Jan 22, 2021

• add installation instructions

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• rename files

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• add timing functions

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• add timing calls to workflow

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• speed up molecule sampling

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• update news, remove alpha

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• update roxygen

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Commits on Jan 25, 2021

• wip scalability vignette

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• add runtime vignette, update other vignettes

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• remove old rds files

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Commits on Jan 26, 2021

• remove r satisfy checks cleanly

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• Fix plot_gold_mappings

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• drop do() as it is superseded, but summarise can handle this functionality now

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• ignore local symlink

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• update scalability vignette

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• update readme

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Commits on Jan 27, 2021

• change combine_models() such that stores more simulations data and also experiment data (if available)

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Commits on Jan 29, 2021

• extend combine_models testing

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• Do not compute dimred if not asked for

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• clean up r cmd check & unname feature info ids

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• add as_SCE() function

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• update news

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• also save logcounts in sce & ad, add small tests to generate_dataset

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• add biocViews: to description in order to get SCE and SummarizedExperiment to install 🤪

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• skip test

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• check whether enough samples are being generated, otherwise generate a warning

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• specify SCE version

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Commits on Feb 1, 2021

• remove duplicate import

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• tweak example

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• factor away r cmd checks

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• add 'as_seurat' conversion function

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• update news and description

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Commits on Feb 2, 2021

• fix rmd check notes

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• fix and expand test

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• disable r 3.6 thanks to seurat

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Commits on Feb 15, 2021

• Rework plotting functions

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• Add dimred plotting function for experiment data

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• drop tf network plot for experiment dimred plot

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• modify disconnected backbone

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• map realcount density on tsimcount density

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• use qc pass to sample realcounts. add some extra statistics to realcounts data frame.

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Commits on Feb 16, 2021

• fix docker pushing

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• fix arg

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• update showcase backbones

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• add vignette for advanced information on tweaking dyngen parameters

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• update news and readme

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Commits on Feb 17, 2021

• initial commit for comparison vignette

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• clean up vignette

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• simplify docs

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• try r-actions

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• also build from devel, for now

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• fix pkgdown config

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• fix double authors in citation entry

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• add helper code for rerendering all vignettes

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• slim down vignettes to reduce execution time for pkgdown

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• wip vignette reruns

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• updating vignettes wip

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• try installing dyno to run pkgdown

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• try installing countsimqc as well

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• update markdowns

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Commits on Feb 18, 2021

• update readme

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• only build pkgdown when pushing to master

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• remove all vignettes since they are hosted on with pkgdown

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• update ignore files

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• update url

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• fix readme

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• clean up figures

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• add link to cmd check badge

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• specify image width

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• fix urls

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• re-enable dyno blocks

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• update vignette, license, metadata

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• update links

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Commits on Feb 19, 2021

• restructure vignettes

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• move files around

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• update paths

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• improve package documentation

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• extend package documentation

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• ship some vignettes in package

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• fix figure heights in vignette

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• prepare for release

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• update news

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• skip testing sce as well

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• propose changes for (not) solving #28.

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Commits on Feb 20, 2021

• wrap_dataset(): Repurpose function to be able to choose the output format using a parameter (#28).

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Commits on Feb 21, 2021

• generate_experiment(): Allow toggling on or off the mapping of the reference library size & CPM distribution.

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• update vignettes

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Commits on Feb 22, 2021

• also return the milestone percentages

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• merge

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• include recent changes in 1.0.0

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• update documentation

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• change format order

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• add more helpful message for now

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• use wrap_dataset() instead of as_dyno() in examples

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• fix format issues

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• update example model

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• simplify combine_models test

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• remove num cores and download cache dir from example model

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• speed up generate partitions check

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• add some more checks for the dataset

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• refactor examples to reduce cmd check time

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• install miniconda

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• update news

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• uniformise examples

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• fix docs

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• don't test plotting functions

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Commits on Feb 23, 2021

• fix vignette

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• fix readme

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