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Syksy / curatedPCaData

Bioconductor R-package: Curated Prostate Cancer Data

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Closed jhcreed closed 3 years ago

jhcreed commented 4 years ago

07-09-2020

[x] for taylor et al. use cbioportal normalization and our own pipeline
[x] create/update vignettes with information on the source of data for each study
[x] create formatting for other clinical vaiables (ex: var_name = var_value | var_name2 = var_value2 | var_name3 = var_value3)

Syksy commented 4 years ago

08-07-2020

Specific details for imputation:

[ ] Median imputation?
[ ] k-NN; how to determine optimal k?
[x] Make sure that rows/columns are correct (assuming that rows are samples, columns are genes)

Immune deconvolution methods:

[x] Determine what are the gene expressions required for each method
[x] Correlate methods with each other and see if they suggest similar compositions
[x] Correlate results with existing results available from e.g. papers
[ ] Leave out CIBERSORT due to registration wall (no R-package/source code available?)

Genes names:

[x] Take the whole list of gene names (biomaRt), save that as a R object inside the package (internal?)
[x] Have all GEX/CNA/... to contain those gene names, even if they're mainly populated with NA values (-> comforming dimensions for genes)

Syksy commented 4 years ago

08-26-2020

Naming conventions

Syksy commented 4 years ago

09-11-2020

Get rid of cBioPortal version of Taylor et al., focus on GEO-derived portion that uses our harmonization discipline
Elaborate further on example analyses
Elaborate further on uses of MultiAssayExperiment (use their examples maybe for inspiration, cheat sheet from https://bioconductor.riken.jp/packages/3.6/bioc/vignettes/MultiAssayExperiment/inst/doc/MultiAssayExperiment_cheatsheet.pdf etc)
Make sure everybody's up to baseline of the master branch (and meet regarding conflicts if a better solution exists than is currently in master)
Figure out which immunedeconv methods can be used with data that's not in TPM GEX-input format (e.g. xCell supporting ranked orders if native package is used?)

Syksy commented 3 years ago

These issues have been now addressed at least for the grand majority, or altered and completed (for example inclusion of CIBERSORT after all).