<commit_before>#+TITLE: bcbioRNASeq
#+STARTUP: content
* Development
** TODO Consider rounding raw counts to integer, matching conventions used
   in internal bcbio-nextgen R script. Non-integer counts tend to confuse
   people. Only want to implement this at gene level.
** TODO Add coercion method support for limma/voom.
** TODO How to get modules out of dendrogram in R?
** TODO pfgsea heatmap code.
** TODO Need to work on the vignettes for Bioconductor submission.
** TODO File an issue with Visual Studio Code repo regarding confusing line
   break behavior with markdown plugin.
** TODO Git inside editor: learn how to master magit (Emacs) and vim-fugitive
   or git-vim (Vim).
** TODO Follow up regarding open issues on GitHub. I have a couple currently.
** TODO Add coercion method support for limma/voom.
** TODO Paper: Switch paper to use `deg()` instead of `significants()`.
** TODO Require valid names in all slots.
** TODO Look into tximeta integration.
** TODO Need to run BFG on the repo and remove old binary commits.
** TODO Relax validity checks to work with v0.2 objects.
** TODO Hide sequencing lanes by default. Remove this message from
   `bcbioRNASeq()` load call: Failed to detect sequencing lanes.
** TODO Consider renaming "normalized" assay to "sizeFactor" or simply "sf".
** TODO plotMeanSD edgeR RLE is messed up for new LnCap data.
** TODO Consider slotting aligned counts into object automatically in
   updateObject call.
** TODO `plotGeneSaturation()`: Consider adding y-intercept 0.
** TODO Remove this message from `bcbioRNASeq()` load call: Failed to detect
   sequencing lanes.
** TODO bcbioRNASeq: Improve error message when user doesn't point to `final/`
   directory. OR make this more flexible and detect `final/` automatically.
** TODO `plotMappingRate()`: Plot exonic, intronic, intergenic rates. Show these
   similarly to qualimap output in MultiQC report.
** TODO `plotCountsPerGene()`: Don't hide the sample legend for `sampleName`
   interesting groups
** TODO Add rsem support for tximport? Is this supported in bcbio?
** TODO Work on additional multiQC-like plots: `plotInsertSize()`,
   `plotDuplicatedReads()`, `plotProperlyPairedReads()`, `plotReadsAligned()`,
   `plotGCContent()`, `plotXYCounts()`.
** TODO Consider saving more elements from shell environment in the object.
    Don't want to save everything because this could stash PAT and other tokens,
    but consider what we'd want to include. PATH may be helpful.
** TODO `updateObject()`: Add update method for run-length encoding in rowRanges.
** TODO `updateObject()`: Improve update handling of `sessionInfo` in metadata?
** TODO Consider adding `as()` coercion support from bcbioRNASeq to limma/voom.
** TODO Inform the user in the QC template which aligner was used for QC
   (e.g. STAR, HISAT2).
** TODO `updateObject()`: Calculate FPKM automatically for gene-level counts
   if missing.
** TODO For PCA labeling, allow the user to specify individual samples in the
   `label` argument, rather than simply using a logical.
** TODO Consider making functions that require DESeqDataSet generation defunct.
    e.g. plotDispEsts, plotMeanSD.
** TODO Double check log2 in plotMeanSD.
<commit_msg>Update the todo list<commit_after>#+TITLE: bcbioRNASeq
#+STARTUP: content
* Development
** TODO Supporting loading of multiple bcbio runs into a single object?
   https://github.com/hbc/bcbioRNASeq/issues/141
** TODO Consider rounding raw counts to integer, matching conventions used
   in internal bcbio-nextgen R script. Non-integer counts tend to confuse
   people. Only want to implement this at gene level.
** TODO Add coercion method support for limma/voom.
** TODO How to get modules out of dendrogram in R?
** TODO pfgsea heatmap code.
** TODO Need to work on the vignettes for Bioconductor submission.
** TODO File an issue with Visual Studio Code repo regarding confusing line
   break behavior with markdown plugin.
** TODO Git inside editor: learn how to master magit (Emacs) and vim-fugitive
   or git-vim (Vim).
** TODO Follow up regarding open issues on GitHub. I have a couple currently.
** TODO Add coercion method support for limma/voom.
** TODO Paper: Switch paper to use `deg()` instead of `significants()`.
** TODO Require valid names in all slots.
** TODO Look into tximeta integration.
** TODO Need to run BFG on the repo and remove old binary commits.
** TODO Relax validity checks to work with v0.2 objects.
** TODO Hide sequencing lanes by default. Remove this message from
   `bcbioRNASeq()` load call: Failed to detect sequencing lanes.
** TODO Consider renaming "normalized" assay to "sizeFactor" or simply "sf".
** TODO plotMeanSD edgeR RLE is messed up for new LnCap data.
** TODO Consider slotting aligned counts into object automatically in
   updateObject call.
** TODO `plotGeneSaturation()`: Consider adding y-intercept 0.
** TODO Remove this message from `bcbioRNASeq()` load call: Failed to detect
   sequencing lanes.
** TODO bcbioRNASeq: Improve error message when user doesn't point to `final/`
   directory. OR make this more flexible and detect `final/` automatically.
** TODO `plotMappingRate()`: Plot exonic, intronic, intergenic rates. Show these
   similarly to qualimap output in MultiQC report.
** TODO `plotCountsPerGene()`: Don't hide the sample legend for `sampleName`
   interesting groups
** TODO Add rsem support for tximport? Is this supported in bcbio?
** TODO Work on additional multiQC-like plots: `plotInsertSize()`,
   `plotDuplicatedReads()`, `plotProperlyPairedReads()`, `plotReadsAligned()`,
   `plotGCContent()`, `plotXYCounts()`.
** TODO Consider saving more elements from shell environment in the object.
    Don't want to save everything because this could stash PAT and other tokens,
    but consider what we'd want to include. PATH may be helpful.
** TODO `updateObject()`: Add update method for run-length encoding in rowRanges.
** TODO `updateObject()`: Improve update handling of `sessionInfo` in metadata?
** TODO Consider adding `as()` coercion support from bcbioRNASeq to limma/voom.
** TODO Inform the user in the QC template which aligner was used for QC
   (e.g. STAR, HISAT2).
** TODO `updateObject()`: Calculate FPKM automatically for gene-level counts
   if missing.
** TODO For PCA labeling, allow the user to specify individual samples in the
   `label` argument, rather than simply using a logical.
** TODO Consider making functions that require DESeqDataSet generation defunct.
    e.g. plotDispEsts, plotMeanSD.
** TODO Double check log2 in plotMeanSD.

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