Scientific Computing issueshttps://git.mpi-cbg.de/groups/scicomp/-/issues2020-10-07T14:53:32Zhttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/19test in pipelines2020-10-07T14:53:32Zdominguetest in pipelinesPipelines to test:
- [x] dge, differential expression
- [x] dge, cp_enrichment
- [x] dge, fgsea
- [x] ms, pre-processing
- [x] ms, dep_tmp
- [ ] sc, QC
- [ ] sc, clustering
- [ ] sc, shinyPipelines to test:
- [x] dge, differential expression
- [x] dge, cp_enrichment
- [x] dge, fgsea
- [x] ms, pre-processing
- [x] ms, dep_tmp
- [ ] sc, QC
- [ ] sc, clustering
- [ ] sc, shinydominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/18Make it public2020-07-20T08:51:12ZdomingueMake it public@henry I can't seem to have enough rights to make this repo public. Could you please do it for me? It is not urgent.@henry I can't seem to have enough rights to make this repo public. Could you please do it for me? It is not urgent.henrydominguehenryhttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/17Missing functions2020-10-30T13:19:00ZdomingueMissing functionsAdd the following functions:
- [x] trim_extAdd the following functions:
- [x] trim_extdominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/16Increase package loading transparency2020-01-09T16:16:39ZdomingueIncrease package loading transparencyRight now once `corescf` is loaded a number of other packages is loaded / installed silently in the background. whilst this might be useful in most of our daily work it is has some side effects such as conflicts with already loaded packa...Right now once `corescf` is loaded a number of other packages is loaded / installed silently in the background. whilst this might be useful in most of our daily work it is has some side effects such as conflicts with already loaded packages and renv (#13).
An alternative solution, which only adds a single line to our workflow is to explicitly call the packages after loading:
```R
library(corescf)
load_packs()
```
This explicit behaviour also makes debugging easier in case of an error. Furthermore, it should print a message with the list of loaded packages.dominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/15Create internal package wepage2020-01-09T15:39:51ZdomingueCreate internal package wepageUsing `pkgdown`. See for example https://jdblischak.github.io/workflowr/
The advantage is that it has an easy overview of all the function - which might not even now exist.
It has to be internal, so I am not sure if that works in gitlab.Using `pkgdown`. See for example https://jdblischak.github.io/workflowr/
The advantage is that it has an easy overview of all the function - which might not even now exist.
It has to be internal, so I am not sure if that works in gitlab.dominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/14Add packages to loading2019-09-26T11:29:40ZdomingueAdd packages to loading`rdoc` for colorized documentation in the command-line:
https://github.com/mdequeljoe/rdoc
`prettycode` to replace the standard print method for functions with one that performs syntax highlighting, using ANSI colors, if the terminal su...`rdoc` for colorized documentation in the command-line:
https://github.com/mdequeljoe/rdoc
`prettycode` to replace the standard print method for functions with one that performs syntax highlighting, using ANSI colors, if the terminal supports them.
https://github.com/r-lib/prettycodedominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/13Initiate renv on load2020-01-09T16:16:57ZdomingueInitiate renv on loadThis would be the easiest way to make sure the `renv` for a project is used.This would be the easiest way to make sure the `renv` for a project is used.dominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/12Load packages on zzz2019-09-26T11:30:07ZdomingueLoad packages on zzzNow that I moved the dependencies to imports these packages are not automatically loaded. Go back to the loading as many packages as possible in zzzNow that I moved the dependencies to imports these packages are not automatically loaded. Go back to the loading as many packages as possible in zzzdominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/11Add code dependencies in functions2020-01-09T15:32:01ZdomingueAdd code dependencies in functionsBasically `@imporFrom` statements to Roxygen. This has two advantages:
- imports only the needed functions from each package thus reducing dependencies;
- makes it clear which functions from which packages are used our package. Easier fo...Basically `@imporFrom` statements to Roxygen. This has two advantages:
- imports only the needed functions from each package thus reducing dependencies;
- makes it clear which functions from which packages are used our package. Easier for maintenance.dominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/10Add travis CI2019-09-06T11:35:04ZdomingueAdd travis CII will make a small mock up and ask Juraj what is missing.I will make a small mock up and ask Juraj what is missing.dominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/9viz: add custom theme2019-09-05T09:16:15Zdomingueviz: add custom themeA publication style one with grids, transparent background, and only lfet and bottom line.A publication style one with grids, transparent background, and only lfet and bottom line.https://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/7Consider adding packages to dependencies2019-09-05T09:00:52ZdomingueConsider adding packages to dependenciesThis would mean missing packages would be installed when `coReSCF` is installed. A few things to keep in mind
- there are many packages which are needed directly for our functions, or indirectly for the workflow and it is hard to know wh...This would mean missing packages would be installed when `coReSCF` is installed. A few things to keep in mind
- there are many packages which are needed directly for our functions, or indirectly for the workflow and it is hard to know which one is which.
- We would need to defined the dependencies' versions, which is good practice for package version control, but it could lead to dependency hell. I would look in the logs of older project to see the minimum required versions. It could be either:
+ `Imports`, which just loads the package or
+ `Depends` which attaches it (similar to calling `library(pkg)`)
- another alternative would be to create a function `load_core` which would need to be called at the start of each script to attach all packages we need for our workflows, instead of having this silently inside `.onAttach`.
I will need some input on this.dominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/6Add tests to functions2019-09-02T09:30:58ZdomingueAdd tests to functionsThis will take some time and we need to define which tests.This will take some time and we need to define which tests.dominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/5Which other scripts are scripts are sourced?2020-01-09T15:32:21ZdomingueWhich other scripts are scripts are sourced?@herseman mentioned that some other scripts are not yet included in the package:
- https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v10/dge_workflow/diffex_commons.R
- https://raw.githubusercontent.com/holgerbrandl/datautils/v1.51/R/core_co...@herseman mentioned that some other scripts are not yet included in the package:
- https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v10/dge_workflow/diffex_commons.R
- https://raw.githubusercontent.com/holgerbrandl/datautils/v1.51/R/core_commons.R
- https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v6/common/cp_utils.R
- https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v10/dge_workflow/diffex_commons.R
- https://git.mpi-cbg.de/bioinfo/datautils/blob/master/R/stats/ci_commons.Rdominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/4Find which functions are not used2019-09-05T09:01:51ZdomingueFind which functions are not usedUse API, and deprecate those that aren't.Use API, and deprecate those that aren't.dominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/3Package name2019-09-05T08:59:20ZdominguePackage nameThe current name is `coReSCF` but I think it could be improved. So @herseman and @henry if you have any suggestions please chip in.The current name is `coReSCF` but I think it could be improved. So @herseman and @henry if you have any suggestions please chip in.dominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/2Test installation from gitlab2019-08-21T11:11:48ZdomingueTest installation from gitlabRight now the package is a private repo on gitlab. Will it install with `devtools::install:gitlab`?Right now the package is a private repo on gitlab. Will it install with `devtools::install:gitlab`?dominguedominguehttps://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/-/issues/1Package creation2019-08-21T09:55:40ZdominguePackage creationThis package was created to document and organize the functions that were previously sourced at the start of each script in our workflows. The code was kept almost entirely as is, so that there is very little risk of breaking existing sc...This package was created to document and organize the functions that were previously sourced at the start of each script in our workflows. The code was kept almost entirely as is, so that there is very little risk of breaking existing scripts, and it was developed by Holger and Lena - I wrapped it in a package and documented it.
Some changes / notes:
- I also also [added](https://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/blob/master/R/zzz.R) `.onLoad()` and `.onAttach()` functions to set `options` and load packages automatically
- The package dependencies were kept at a minimum, but it will attempt to install / load all the packages we need - this was already done silently when sourcing the R helpers.dominguedomingue