Alyssa Frazee comments

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                                            Alyssa Frazee

sampleNames issue

maybe make user supply sampleNames if they use "samples" in ballgown

sampleNames issue

be more flexible about how sampleNames is assigned (don't rely on directory structure having sample name right above .ctab files)

more "global" visualization functions?

Ballgown isn't currently under active development by the creators -- the philosophy right now is bugfixes only. But we're open to community contributions!

feature requests for plotTranscripts: use gene names; plot multiple genes at once

Hey, sorry for the delay here, and thanks for the feature requests! For the first two questions (plotTransactions being compatible with annotation gene names and plotting of multiple genes at...

Feature request: subset does not handle exon and intron expression

Hi there, thanks for the note! I responded on Bioconductor with a workaround that should unblock you. Currently ballgown is maintenance mode only (bugfixes only, no new features) but if...

Yo. IDEA.

I like it! Two thoughts: first, maybe we could incorporate an "all" checkbox into this legend (and then perhaps not have to deal with the current "Raw Repo Counts" checkbox)....

plotMeans set par(mfrow(c=(x,y))

Thanks for the feedback! We can probably do this. cc @JMF47

Error in using a lot of gene ids to subset bg object

could you please post the exact command you ran that gave you the error? thanks!

getGenes can't find subjectHits

Interesting: it looks like `subjectHits` was removed from the `S4Vectors` package in 0.12 (and renamed to `to`): https://github.com/Bioconductor-mirror/S4Vectors/blob/master/NEWS#L99 I'll bump the version requirement in ballgown and write a test for...

NANs pvalues and qvalues

Hey, really sorry for the long delay. This is a question that's probably better for support.bioconductor.org with the "ballgown" tag, since that's where analysis questions tend to get answered faster....