SIAMCAT issueshttps://git.embl.de/grp-zeller/SIAMCAT/-/issues2018-08-13T06:57:52Zhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/93Create tax table from appropriate feature names2018-08-13T06:57:52ZJakob WirbelCreate tax table from appropriate feature names## Summary
Create a tax table automatically from feature names that contain this information, i.e. k__;p__;g__ and so on
## Affected functions/datasets/objects
`summarize.features`
/cc @zych## Summary
Create a tax table automatically from feature names that contain this information, i.e. k__;p__;g__ and so on
## Affected functions/datasets/objects
`summarize.features`
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/44Evolve to tidyverse2018-02-26T06:18:25ZKonrad ZychEvolve to tidyverse- [ ] elapsed time formatted with lubridate
- [x] documentation website with pkgdown
- [ ] ...- [ ] elapsed time formatted with lubridate
- [x] documentation website with pkgdown
- [ ] ...https://git.embl.de/grp-zeller/SIAMCAT/-/issues/101Feature request for check.associations2019-02-07T10:33:49ZKonrad ZychFeature request for check.associationsadd an option to use paired=TRUE in `wilcox.test`
add an option to use paired=TRUE in `wilcox.test`
https://git.embl.de/grp-zeller/SIAMCAT/-/issues/106Feature request: warning if the species are too long to fit on the associatio...2019-11-01T11:35:46ZJakob WirbelFeature request: warning if the species are too long to fit on the association plotpretty well described in the title...pretty well described in the title...https://git.embl.de/grp-zeller/SIAMCAT/-/issues/98Figure out how to take care of the Rscript flavor2018-10-01T19:16:47ZKonrad ZychFigure out how to take care of the Rscript flavorShould it stay out of the Bioconductor or should we add it?Should it stay out of the Bioconductor or should we add it?https://git.embl.de/grp-zeller/SIAMCAT/-/issues/104include feature weights in the models slot of the siamcat object?2019-09-17T14:15:25ZJakob Wirbelinclude feature weights in the models slot of the siamcat object?include the feature weights and weights table in different slots in the models slot of the siamcat object for easier access
for models trained on gene group abundance data, the retrieval of feature weights takes forever and could be spe...include the feature weights and weights table in different slots in the models slot of the siamcat object for easier access
for models trained on gene group abundance data, the retrieval of feature weights takes forever and could be sped up by saving the tables directlyJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/20Log R-script run into Rmd file2018-02-12T14:14:57ZKonrad ZychLog R-script run into Rmd fileThe log of R-script flavor execution should land in one neat R markdown file :ok_hand_tone1:
- [ ] each file starts with ##heading with name of the function\
- [ ] ###heading: paramaters of the run
- [ ] all the parameters of the run are...The log of R-script flavor execution should land in one neat R markdown file :ok_hand_tone1:
- [ ] each file starts with ##heading with name of the function\
- [ ] ###heading: paramaters of the run
- [ ] all the parameters of the run are saved :floppy_disk: there
- [ ] ###heading: results of the run
- [ ] all the verbose results of the run
- [ ] (optional): parameter for the user to choose screen/RmdPublicationKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/102NEWS for Release 3.92019-04-25T09:03:08ZKonrad ZychNEWS for Release 3.9* Bugfix for add.meta.pred function
* Bugfix for confounder-check function
* Included vignette figures in man/figure
* Bugfix for summarize.features function
* Bugfix for siamcat creator function
* Fixed centered log ratio transform to b...* Bugfix for add.meta.pred function
* Bugfix for confounder-check function
* Included vignette figures in man/figure
* Bugfix for summarize.features function
* Bugfix for siamcat creator function
* Fixed centered log ratio transform to be per sample and not per feature
/cc @jawirbel @zeller @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/77Prune metadata function2018-05-17T10:09:42ZKonrad ZychPrune metadata function### Summary
A new function to prune metadata.
/cc @zych### Summary
A new function to prune metadata.
/cc @zychPublicationKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/54Unit testing2018-04-16T11:34:55ZKonrad ZychUnit testing### Summary
Add unit testing to SIAMCAT with [testthat](http://testthat.r-lib.org/index.html)
### Useful link
http://bioconductor.org/developers/how-to/unitTesting-guidelines/
/cc @zych### Summary
Add unit testing to SIAMCAT with [testthat](http://testthat.r-lib.org/index.html)
### Useful link
http://bioconductor.org/developers/how-to/unitTesting-guidelines/
/cc @zychKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/27Update galaxy interface2018-04-17T09:42:48ZKonrad ZychUpdate galaxy interface- [ ] incorporate latest version
- [ ] test
- [ ] :package: ship it- [ ] incorporate latest version
- [ ] test
- [ ] :package: ship itPublicationhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/78Vignette - advanced workflow/optional modifications2018-05-17T10:07:55ZKonrad ZychVignette - advanced workflow/optional modifications### Summary
Vignette summarizing additional options/modifications to the workflow and troubleshooting.
### Modifications
- [ ] filtering
- [ ] normalization
- [ ] machine learning approaches
- [ ] visualizations
### Troubleshooting
- ...### Summary
Vignette summarizing additional options/modifications to the workflow and troubleshooting.
### Modifications
- [ ] filtering
- [ ] normalization
- [ ] machine learning approaches
- [ ] visualizations
### Troubleshooting
- [ ] no significant associations
- [ ] not enough data
/cc @zychPublicationhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/21Visualization with iTOL2018-02-19T20:12:10ZKonrad ZychVisualization with iTOL- [ ] making sure we know how to easily integrate those two tools :recycle:
- [ ] output of the model in a format that iTOL can easily use :deciduous_tree:- [ ] making sure we know how to easily integrate those two tools :recycle:
- [ ] output of the model in a format that iTOL can easily use :deciduous_tree:PublicationKonrad ZychKonrad Zych