Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

1 sequences (1 circular) from hg38 genome > > Everything is mapped via the GENEID, and if you query the UCSC genome > browser for hg38/knownGene, asking for gene name, known gene ID and gene > symbol, you will get the first and last but not the middle. > > > > -Original Messa

Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

, "GENEID", "CDSCHROM", "SYMBOL")) > 'select()' returned 1:1 mapping between keys and columns >SYMBOLGENENAME CDSCHROMGENEID > 1 MTCYBP1 MT-CYB pseudogene 1 100499418 > > relevant? > > On Thu, Mar 28, 2024 at 9:17 AM

Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

Hi Lori and fellow maintainers, I had a strange experience yesterday where I pulled down genes and transcripts from Homo.sapiens, only to discover that all mitochondrial encoded genes (MT-CYB, MT-CO2, etc) were missing. Is there an historical reason why this is so? Obviously these transcripts

Re: [Bioc-devel] igvR and igvShiny - anyone interested in taking ownership?

Argh, I emailed the wrong person! If you can’t find a less frazzled person to take over igvR, I’d be happy to. It’s a great package and very useful to us. Cheers and congratulations! --t > On Aug 15, 2023, at 2:09 PM, Paul Shannon > wrote: > > Dear Bioconductor Developers, > > As I retire

Re: [Bioc-devel] Memory error from sesame build

Recursion issue. Make sure some constructor isn’t constructing itself into oblivion. This is a nasty one --t > On Nov 27, 2021, at 5:48 AM, Zhou, Wanding > wrote: > > Hi, > Recently we are experience some memory issue on both development and release > (mostly Windows) that causes the sesam

Re: [Bioc-devel] Adding new "DifferentialDNA3DStructure" to biocViews

Seconded HiC isn’t even very good at this 😁 --t > On Apr 3, 2021, at 7:05 AM, Matthias Zytnicki > wrote: > > Dear everyone, > > > First please accept my apologies if my request is not appropriate here. > > If so, please suggest me how to proceed. > > > I would like to suggest adding a

Re: [Bioc-devel] New package Vignette

The vignette shows up when I visit Looks like a useful package. --t > On Aug 21, 2020, at 1:54 PM, Shepherd, Lori > wrote: > > Thank you for reaching out. Since the package just became available please > allow a few days for everything to populate on the builders and landing pages. > We w

[Bioc-devel] credentials/authors for MTseeker, biscuiteer, and data packages corresponding to each

Hi Nitesh, I'm the actual maintainer of MTseeker and the person who currently gets emails about biscuiteer. However, Jacob Morrison is the person who actually maintains biscuiteer. At some point my credentials for bioc-git seem to have become interchanged with jacob's, and when I went to fix thi

Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

ot;) > Error in mapIds(Homo.sapiens, names(gxs), "SYMBOL", "ENTREZID") : > could not find function "mapIds" > > Where can I find this function? > > > SomeGenes <- gxs[ c("HRAS", "WT1", "IGF2") ] > Error: object

Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

> Error in genes(Homo.sapiens) : could not find function "genes" >> >> Renaming Homo.sapiens as BSgenome.Hsapiens.UCSC.hg19 did not work. Should I >> look up how this genome is called? >> >> >> > names(gxs) <- mapIds(Homo.sapiens, names(gxs), &

Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

"test.bam" > bf <- BamFile(bamfile) > param <- ScanBamParam(which=GRanges(c("4", "9"), IRanges(start=c(55599321, > 5073770), end=c(55599321, 5073770 > > Now, I want to perform this on more than 1 bam file at once and on more > region. > >

Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

think it will become a useful exercise. --t > On Mar 5, 2020, at 4:36 PM, Tim Triche, Jr. wrote: > >  > a few thoughts: > > 1) look into Shearwater > (https://bioconductor.org/packages/release/bioc/html/deepSNV.html), then > > 2) talk to Todd Druley @ WashU, Elli

Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

and answers. I can certainly look > into the package, although this may be unsuitable for me as I used targeted > NGS. > > For additional questions I will contact #2. > > Thanks, > > René > > Van: Tim Triche, Jr. [mailto:tim.tri...@gmail.com] > Verzonden:

Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

a few thoughts: 1) look into Shearwater ( https://bioconductor.org/packages/release/bioc/html/deepSNV.html), then 2) talk to Todd Druley @ WashU, Elli Pappaemanuil @ MSKCC, Ruud & Bob @ Erasmus, the usual suspects 3) plan to validate w/ddPCR (at the absolute very least) and be aware that most MR

Re: [Bioc-devel] New SE or new assay in SE?

Assume the object is backed by an HDF5 or Zarr array, for the sake of argument and because that’s kind of how it works these days for many people. Also assume the “SE*” may not actually be an SE, but rather some wacky subclass of SE. If you return a new SE*, you need to copy all the metadata,

Re: [Bioc-devel] Git pushing problems for data package

have access to maintain the repositories that I am maintaining. So if you could counsel me on how to fix that, it would be awesome, because I've run out of ideas on my end :-/ Thanks so much! --t On Sun, Nov 17, 2019 at 4:19 PM Tim Triche, Jr. wrote: > This is suboptimal: >

Re: [Bioc-devel] Git pushing problems for data package

This is suboptimal: Email: tim.tri...@gmail.com GitHub Username: jamorrison As you might imagine, I am not Jacob and Jacob is not me. I'm wondering how this happened? --t On Sun, Nov 17, 2019 at 4:17 PM Tim Triche, Jr. wrote: > I went to the git login checker, and activated m

Re: [Bioc-devel] Git pushing problems for data package

hyAnalysis So that doesn't seem like a good thing either. I'm getting progressively more confused the deeper I look :-/ --t On Sun, Nov 17, 2019 at 3:46 PM Tim Triche, Jr. wrote: > Actually, it seems to have somehow got worse?! > > $ cd MTseeker > $ git push upstream

Re: [Bioc-devel] Git pushing problems for data package

exists. Now it seems as if all repositories are using t.triche for access somehow? Perhaps I have misconfigured something somewhere. I will look into this... but my github SSH keys are all for `ttriche` not `t.triche`. --t On Sun, Nov 17, 2019 at 3:21 PM Tim Triche, Jr. wrote: > Hi Nit

Re: [Bioc-devel] Git pushing problems for data package

. $ grep Version MTseekerData/DESCRIPTION Version: 1.5.2 $ grep Version MTseekerData.bioc/DESCRIPTION Version: 1.5.0 $ grep name ~/.gitconfig name = ttriche I'm out of ideas ... --t On Fri, Nov 15, 2019 at 11:09 AM Tim Triche, Jr. wrote: > Thanks Nitesh! Not sure how that happ

Re: [Bioc-devel] Git pushing problems for data package

ed the issue. You are now universally "ttriche" only. > > You should have access now. > > Best > > Nitesh > >> On Nov 15, 2019, at 9:52 AM, Tim Triche, Jr. wrote: >> >> Hi all, >> >> How do I push changes to my MTseekerData package in

[Bioc-devel] Git pushing problems for data package

Hi all, How do I push changes to my MTseekerData package in git? I get the following error when I try to commit changes: tim@tim-ThinkPad-T470:~/Dropbox/MTseekerData$ git remote -v origin g...@github.com:trichelab/MTseekerData.git (fetch) origin g...@github.com:trichelab/MTseekerData.git (pus

Re: [Bioc-devel] Call for collaborators/advice

Maybe the question arises whether to store a reduced representation like, say, singleCellExperiment does? In any event, I agree that endomorphism will be expected by users and, like tximport collapsing many transcripts into each gene, the sensible thing to do is just to return a binned (less ro

[Bioc-devel] submitting a tiny data package (GmapGenome.Hsapiens.rCRS)

What's the best/fastest way to do this? The package (MTseeker) will happily build and install it for the user via the indexMTgenome() function, but since I test for its presence prior to running examples, it seems like I might as well have it available through BioC. Thanks, --t [[alterna

Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

forms. Don't know how easy it would be to use to achieve > the kind of variant calling you're doing in MTseeker though... > > Cheers, > H. > > On 10/11/2018 04:35 AM, Tim Triche, Jr. wrote: > > This makes sense. Windows users won’t be easily able to call variants

Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

re. >> So MTseeker will be supported and available on all platforms. >> For MTseekerData: the package doesn't seem to make any use of gmapR >> so you can probably remove gmapR from its Suggests field. >> Hope this helps, >> H. >>> On 10/10/2

[Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

it looks like gmapR does not support Windows, and as a result, my MTseeker package cannot build on tokay1, so the Data package which requires it also cannot build on tokay1. Are there platform-specific dontrun capabilities? http://bioconductor.org/spb_reports/MTseekerData_buildreport_201810101032

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

with more detail on handling packages with mutual (circular) dependencies. > I see your package was assigned to Herve - if you are still having problems > with the build you can ask @lshep or @hpages for help on the issue. > > Thanks for the pull request, it's been merged. > >

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

rs, > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Bioc-devel on behalf of > Obenchain, Val

[Bioc-devel] avoiding circular dependencies between a Data package and a Software package

Last night I submitted MTseeker and its companion package MTseekerData, both festooned with examples that run smoothly and pass BiocCheck. HOWEVER! Breaking up the data into a Data package inadvertently seems to have created a circular dependency between the Software and Data packages. I haven't h

Re: [Bioc-devel] Error: file larger than 5 Mb.

hmm, does it make sense to submit the hg19, hg38, and mm10 HMM CpG island predictions to AnnotationHub? R> qhs <- query(ah, "island" ) R> qhs AnnotationHub with 4 records # snapshotDate(): 2018-08-20 # $dataprovider: UCSC # $species: Homo sapiens # $rdataclass: GRanges # additional mcols(): taxono

Re: [Bioc-devel] Question

Vince beat me to it. Don’t use Kent utils unless you have to. If you have something like a bigBed parser, I could perhaps help clean it up. But if you’re doing anything that could possibly be done in Rsamtools or rtracklayer, I would join Vince in urging you to use their functions. You will have

[Bioc-devel] sessionInfo() breaks the 5000-character limit on support.bioconductor.org

This seems like a bug, since sessionInfo() is requested, but simply cut-and-pasting my sessionInfo() output breaks the character limit for the support site. I suppose I can also post a support question about this... the original motivation was to document a bizarre failure mode where ExperimentHub

Re: [Bioc-devel] EXTERNAL: introducing BiocManager in devel package pages?

ls.html > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------ > *From:* Bioc-devel o

[Bioc-devel] introducing BiocManager in devel package pages?

So I was looking at DropletUtils and stumbled on this: To install this package, start R and enter: ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R";) biocLite("DropletUtils") It seems like maybe devel might be a sensible place to start migrating use

Re: [Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

packages: foreign, > MASS, mgcv, survival > > Update old packages: 'openssl', 'stringi' > > Update all/some/none? [a/s/n]: > > n > > Warning message: > > In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : > > install

Re: [Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

BiocManager::install(whatever) doesn't work? biocLite is supposed to die, you see... --t On Mon, Jul 30, 2018 at 2:45 PM Leonardo Collado Torres wrote: > Hi bioc-devel, > > A co-worker of mine (Richard) tried several times to install the > DelayedArray package. We got a couple of errors but

[Bioc-devel] typo on website 'install' page

On the Install page, https://www.bioconductor.org/install/, I just noticed that in the box on the right hand side, the "Worflow packages" link is misspelled (missing 'k'). --t [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org ma

Re: [Bioc-devel] Suggested edits to support site posting guide

well, Hadley usually walks people through the steps required to 1) file a bug reproducibly or 2) learn how to do the thing in question organically, and his universe is doing OK, so N=1 in favor of that approach. Also a lot of people helped me learning Perl (!) on Usenet (!!!) so yeah I'm old but i

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

themselves. > > Pete > > > > On Mon., 30 Apr. 2018, 12:11 pm Tim Triche, Jr., > wrote: > >> But if you merge methods like that, the error method can be that much more >> difficult to identify. It took a couple of weeks to chase that bug down >> properly, a

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

seemingly simple abstractions appear to require more thought. That was my only point. --t On Mon, Apr 30, 2018 at 11:28 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > But that issue will be fixed, so Tim's advice is inappropriate. > > > On 04/30/201

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

Don't do that. Seriously, just don't. https://github.com/Bioconductor/DelayedArray/issues/16 --t On Mon, Apr 30, 2018 at 10:02 AM, Elizabeth Purdom < epur...@stat.berkeley.edu> wrote: > Hello, > > I am trying to extend my package to handle `HDF5Matrix` class ( or more > generally `DelayedArray

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

Moving it to Suggests: would certainly ease installation on clusters and such. --t On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 01/24/2018 03:38 PM, Wolfgang Huber wrote: > >> GenomicFeatures_1.31.3 imports RMySQL. >> >> I'm having great trouble ins

Re: [Bioc-devel] 'IlluminaHumanMethylation450k.db' package installation

1) It's supposed to be deprecated -- I'm not 100% sure why it's still in release :-/ but will look into that 2) the FDb.InfiniumMethylation.hg19 package and (eventually-forthcoming-when-I-get-around-to-it) FDb.InfiniumMethylation.hg38 package are meant as its successor[s], hence the error message:

Re: [Bioc-devel] "extra" unit tests

Emphatic +1 --t > On Oct 25, 2017, at 9:56 AM, Kasper Daniel Hansen > wrote: > > I think we need to think about this in the long term. Can we add support > for these major tests in the build system, perhaps not every day, but every > week or month? The alternative, that it is up to the develo

Re: [Bioc-devel] MultiAssayExperiment compared to SummarizedExperiment (was: Why should Bioconductor developers re-use core classes?)

And/or MAE : SE :: Ragged : Tidy ;-) --t On Thu, Oct 19, 2017 at 10:27 AM, Tim Triche, Jr. wrote: > MAE : SE :: Tensor : Matrix > > --t > > On Thu, Oct 19, 2017 at 10:16 AM, Levi Waldron < > lwaldron.resea...@gmail.com> wrote: > >> On Wed, Oct 18, 2017 at 8

Re: [Bioc-devel] MultiAssayExperiment compared to SummarizedExperiment (was: Why should Bioconductor developers re-use core classes?)

MAE : SE :: Tensor : Matrix --t On Thu, Oct 19, 2017 at 10:16 AM, Levi Waldron wrote: > On Wed, Oct 18, 2017 at 8:00 PM, Dario Strbenac < > dstr7...@uni.sydney.edu.au> > wrote: > > > Good day, > > > > It might be useful to readers to have a comparison table (ticks and > > crosses) in the MultiA

Re: [Bioc-devel] Query regarding size limit and including external datasets

Any TCGA MAFs released to the public were considered deidentified. That wouldn't be the part i would worry about. It's a nice idea, and a data package or packages seems like the idiomatic way to do it, as you noted. Personally I think it would indeed benefit a lot of people (vs, say, GDC). Mafto

[Bioc-devel] "chartr" method for MaskedXString objects with active masks not ready yet Please complain!

Hey I'm just doing what I'm told... any easy/obvious thing for me to fix? I can submit a patch if I know what style is expected... I do need this sort of functionality, as it happens. R> as.character(stubbed[1]) ANKMY1 "chr2:240418839-242500275:-" R> CGmasked <- maskMotif(ge

[Bioc-devel] requireNamespace() / loadNamespace() vs. Imports: / Depends: / Suggests:

Today I stumbled across requireNamespace() as a suggested approach to managing sprawling dependencies, particularly in packages that are meant to be "core" building blocks in e.g. BioC. http://r-pkgs.had.co.nz/namespace.html My reading (which may be very, very far off) is that when a desirable pi

Re: [Bioc-devel] any interest in a BiocMatrix core package?

yes the DelayedArray framework that handles HDF5Array, etc. seems like the right choice? --t On Fri, Feb 24, 2017 at 1:26 PM, Aaron Lun wrote: > Hi everyone, > > I just attended the Human Cell Atlas meeting in Stanford, and people were > talking about gene expression matrices for >1 million ce

Re: [Bioc-devel] package review help

the JOSS process is a nice template that could be expanded and potentially "crowdsourced" without causing chaos (by virtue of its items being mostly independent of each other): https://github.com/openjournals/joss-reviews/issues/27#issue-159802506 --t On Fri, Sep 30, 2016 at 9:05 AM, Michael La

Re: [Bioc-devel] GEOquery for Bioc devel

GEOmetadb had an issue with Dropbox jerking around URLs (cf https://github.com/ttriche/simpleSampleSearch/blob/master/R/checkForUpdates.R ); I wonder if this might be related? I'd hate for GEO to become as flaky as biomaRt. I should have submitted simpleSampleSearch for 3.3 but it seemed too t

Re: [Bioc-devel] Feedback on OrganismDb development

On Thu, Apr 7, 2016 at 11:24 AM, Tim Triche, Jr. >> wrote: >> Great! This is an awesome opportunity to move to ENSEMBL as a default ;-) >> (only half kidding, by the way) >> >> 1) BSGenome/2bit would be great -- I use this sometimes to generate fusion >> tr

Re: [Bioc-devel] Feedback on OrganismDb development

Great! This is an awesome opportunity to move to ENSEMBL as a default ;-) (only half kidding, by the way) 1) BSGenome/2bit would be great -- I use this sometimes to generate fusion transcripts with defined breakpoints to supplement existing txomes 2) class name: don't change it 3) pre made pa

Re: [Bioc-devel] License question for experimental data package

cently when wanting to publish european data from a web > database. > >> On Mar 4, 2016 10:05 AM, "Tim Triche, Jr." wrote: >> Data (facts) are not copyright worthy, but databases (collections of facts) >> can be. See Feist v Rural for precedent; in short, t

Re: [Bioc-devel] License question for experimental data package

Data (facts) are not copyright worthy, but databases (collections of facts) can be. See Feist v Rural for precedent; in short, there must be an inobvious and creative aspect to the database for it to be elevated to copyrightable status. I doubt that a collection of datasets would clear this ba

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

ENSEMBL knownGene was always a disaster. For extra amusement/horror, be sure to check out the sad saga of the TCGA GAF and its disconnection from knownGenes as well as reality. Three cheers for rendering transcript-level estimates useless (and no this was not Katie's fault) Rainer and many othe

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

Also things like organismdbi don't seem to exist for organisms other than human, mouse, rat. So if you want to use that infrastructure for fly or worms, you're SOL at the moment. This is a highly topical discussion since many/most microarray probes can be profitably (in terms of knowledge, no

Re: [Bioc-devel] Common workflow to build an microarray annatation package, like hgu133a.db

ve been wrong many times before. Hopefully by documenting the various ways in which I've tried doing things (right and wrong), there can be some benefit to others trying the same. Best, --t On Tue, Jan 5, 2016 at 5:11 PM, James W. MacDonald wrote: > > On Jan 5, 2016

Re: [Bioc-devel] Common workflow to build an microarray annatation package, like hgu133a.db

1) this is a support.bioconductor.org question 2) don't use .db0 packages, you will rue the day you did best, --t On Tue, Jan 5, 2016 at 3:53 PM, Zhilong Jia wrote: > Hello, > > Happy new year. > > What is the common work-flow to build an microarray annotation package, > like hgu133a.db. > > F

Re: [Bioc-devel] Base class for interaction data - expressions of interest

Metoo. This is becoming an item of major interest for some treatment biomarkers we are studying. --t > On Nov 7, 2015, at 11:33 AM, Morgan, Martin > wrote: > > Just to say that this is a great idea. If this starts as a github package (or > in svn, we can create a location for you if you'd l

Re: [Bioc-devel] SummarizedExperiment with alternate back end

bigmemoryExtras (Peter Haverty's extensions to bigMemory/bigMatrix) can be handy for this, as it works well as a backend, especially if you go about splitting by chromosome as for CNV segmentation, DMR finding, etc. It's not as seamless as one might like, but it's the closest thing I've found. S

Re: [Bioc-devel] as.character method for GenomicRanges?

rad, I was just about to say, "hey, I've written that function in 3 different places, I think I could send in a patch..." and then of course Herve is on it. I need to remember to leave things to the professionals... --t On Tue, Sep 15, 2015 at 10:38 AM, Hervé Pagès wrote: > Hi Michael and Mich

[Bioc-devel] http://bioconductor.org/about/core-team/ could probably stand an update

for geography if nothing else :-) --t [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] annoSet?

two thoughts 1) the ChromImpute calls come from individually ensemble-imputed tracks which together suggest a state N with probability p, such that p(N) = 1-p(!N) and in some cases p may be rather less than 1 for a given span of ~200bp. The uncertainty in state assignments is actually of interest

[Bioc-devel] SSL support in Docker images?

Hi all, I was looking to see whether my proposed DMRcate changes would run smoothly within the devel_microarray Docker image, and ran into this blocker (below). So I can't use install_github to see whether the addition of the changes I've proposed will integrate smoothly with the devel docker ima

Re: [Bioc-devel] RangedSummarizedExperiment

Let the record show that it was relatively trivial to add a generic function called update() to fix the broken serialized instances of the older SE-descendant classes that now inherit from RSE... Although it was a drag until I got around to writing those. I'll try to put together a decently sized

Re: [Bioc-devel] RangedSummarizedExperiment

Hey since the refactoring is already breaking stuff willy nilly, can I make a few suggestions? 1) please for the love of all that is holy have backwards compatible methods for RSEs. It's excruciating to have RSE as the target class, supporting RELEASE users with SE, and have to do endless duck

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

t; > At the risk of annoying Herve further, what about > > > > gr <- castSeqInfo(gr, "gh19") > > gr! > > > > > ? > > > > ~G > > > > On Fri, Jun 5, 2015 at 1:46 PM, Tim Triche, Jr. > <mailto:tim.tri...@gmail.com>

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

maybe standardizeSeqinfo or fixSeqinfo is clearer after all Statistics is the grammar of science. Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science> On Fri, Jun 5, 2015 at 1:41 PM, Gabe Becker wrote: > > > On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr. > wro

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

with 4 sequences (1 circular) from hg19 genome: >>>>>># seqnames seqlengths isCircular genome >>>>>># chr2243199373 FALSE hg19 >>>>>># chrX155270560 FALSE hg19 >>>>>

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

m6, dm3, ce10, ce6, ce4, ce2, sacCer3, > > and sacCer2. I'll add more. > > > > See ?Seqinfo for some examples. > > > > Right now it fetches the information from internet every time you > > call it but maybe we should just store that information in the > > Ge

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

ent, they just coordinate > interactions with packages that you'll already have. > > On Wed, Jun 3, 2015 at 3:26 PM, Tim Triche, Jr. > wrote: > >> Right, I typically do that too, and if you're working on human data it >> isn't a big deal. What makes th

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

at this information is present in the BSgenome packages, >> but it seems (to me) to be very appropriate to have them around for >> cleaning up the seqinfo slot. For some situations it is not great to >> depend on 1 GB> download for something that is a few bytes. >> >>

[Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

It would be nice (for a number of reasons) to have chromosome lengths readily available in a foundational package like GenomeInfoDb, so that, say, data(seqinfo.hg19) seqinfo(myResults) <- seqinfo.hg19[ seqlevels(myResults) ] would work without issues. Is there any particular reason this couldn't

Re: [Bioc-devel] exptData(SummarizedExperiment)

t;> > > > >> H. > > > >> > > > >> > > > >> On Mon, May 11, 2015 at 5:10 PM, Hervé Pagès > > > >> mailto:hpa...@fredhutch.org> > > > >> <mailto:hpa...@fredhutch.org <mailto:hpa...@fre

Re: [Bioc-devel] exptData(SummarizedExperiment)

for exptData() on > RangedSummarizedExperiment objects. It's on my list to add > an exptData method for backward compatibility. > > Cheers, > H. > >> On 05/11/2015 04:37 PM, Tim Triche, Jr. wrote: >> who determined that breaking this would be a good idea?!? >>

[Bioc-devel] exptData(SummarizedExperiment)

who determined that breaking this would be a good idea?!? R> ?SummarizedExperiment Help on topic 'SummarizedExperiment' was found in the following packages: Package Library GenomicRanges /home/tim/R/x86_64-pc-linux-gnu-library/3.2 SummarizedExperiment

Re: [Bioc-devel] BrowserViz and sub-protocols

ne promises), and > supports incremental reads, with mmap, etc. Just seems a little out there. By > the guy who designed protobufs v2. > > >> On Mon, Apr 6, 2015 at 5:08 PM, Dan Tenenbaum wrote: >> >> >> ----- Original Message - >> > From: &q

Re: [Bioc-devel] BrowserViz and sub-protocols

Protobuf begat Avro (more or less) https://avro.apache.org/docs/current/#compare --t > On Apr 6, 2015, at 5:08 PM, Dan Tenenbaum wrote: > > > > - Original Message - >> From: "Michael Lawrence" >> To: "Tim Triche, Jr." >> Cc: &qu

Re: [Bioc-devel] BrowserViz and sub-protocols

Kitware seems to have had good experiences with WAMP, which is a good sign, given the complexity of their typical visualization projects (stemming from old HPC projects in fluid dynamics, astrophysics, realtime anatomical reconstruction, etc). Thus WAMP seems like a great way to leverage the ex

Re: [Bioc-devel] new package: canceR

So use mclust to fit a mixture model? (for one gene or exprs%*%coefs) e.g. mc <- Mclust(exprScoreOrWhatever) plot( survfit( Surv(EFS, EFSevent) ~ mc$class ) ) This is from memory but done often. Seems not too hard to add...? --t > On Mar 26, 2015, at 9:00 PM, Dario Strbenac > wrote: > > An

Re: [Bioc-devel] Short URLs for packages?

s such, for instance if only in devel > when the paper is being written as .../3.1/..., but that there is no > substantive cost to also referencing 'current version available [after April, > 2015] at .../release/ > > > 5. At the end of the day I find myself casting

Re: [Bioc-devel] Short URLs for packages?

t; > On March 23, 2015 9:18:57 AM PDT, "Tim Triche, Jr." > wrote: > > > >> Packages are (read: should be, IMHO) published, citable pieces of > >research, though. Imagine if a paper you cite were silently updated > >without the doi/citation changing. That

Re: [Bioc-devel] Short URLs for packages?

> I guess my problem is that there is even an "if" at the beginning of that > sentence. That's not an attack on you, I know that the above reflects the > current state of affairs, I'm simply saying that perhaps Bioconductor, as a > project, can help/encourage people to do better. Quite true.

Re: [Bioc-devel] Short URLs for packages?

> Packages are (read: should be, IMHO) published, citable pieces of research, > though. Imagine if a paper you cite were silently updated without the > doi/citation changing. That wouldn't be good I don't disagree, but the existing setup does nothing to address that. Citation('limma'), for ex

Re: [Bioc-devel] Short URLs for packages?

.../release/... silently changes every six months or so, as does .../devel/..., so I don't see how this changes anything beyond that. It does make finding the packages a lot easier in general, and more mnemonic. If you want to document the versions of packages used in an analysis, there's alw

Re: [Bioc-devel] requirement for named assays in SummarizedExperiment

be my memory is not serving me well in this case. Is that the issue? Thanks, --t > On Mar 12, 2015, at 9:24 AM, Martin Morgan wrote: > >> On 03/12/2015 08:12 AM, Tim Triche, Jr. wrote: >> What he said >> >> This doesn't make any sense from an API perspectiv

Re: [Bioc-devel] requirement for named assays in SummarizedExperiment

What he said This doesn't make any sense from an API perspective. When would a user ever expect to see unnamed assay matrices? --t > On Mar 12, 2015, at 7:46 AM, Kasper Daniel Hansen > wrote: > > allowing positional matching strikes me as being far too fragile. > Depending on the actual imp

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

container design we > are talking about in this thread addresses the management of a fixed > common assay type over a fixed set of samples. > > The biocMultiAssay deals with the management of multiple assay types over > multiple samples, with possible > disparities in sample se

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

t;> >>>> There are some nice similarities in these new imaginary types. A >>>>> "GRangesFrame" is a list of dimensionally identical things (columns) >>>>> and >>>>> some row meta-data (the GRanges). The SE-like object is similarl

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

ussion are IMO similar to the ones for > biocMultiAssay: > > https://github.com/vjcitn/biocMultiAssay > > maybe Vince can confirm. > > robert. > > On 03/04/2015 05:16 PM, Tim Triche, Jr. wrote: > > Oh, I don't disagree. Perhaps the two problems can be address

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

ition in the >> >> generic >> >> signature). Then, once all of the methods have been assigned for a >> >> particular class, it is made to inherit from that contract class. There >> >> are >> >> lots of gotchas though. Not sure how useful it woul

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

This. It would be damned near perfect as a return value for assays coming out of an object that held several such assays at several time points in a population, where there are both assay-wise and covariate-wise "holes" that could nonetheless be usefully imputed across assays. Statistics is the

Re: [Bioc-devel] January 2015 newsletter

This is great. I've been wanting an excuse to play with csaw; it is a logical complement to the derFinder package (which implements a similarly annotation-agnostic approach to differential expression from RNAseq data). Yet more time saved not implementing methods that someone else (eg Smyth's gr

Re: [Bioc-devel] SummarizedExperiment vs ExpressionSet

so as a simple experiment, I did the following: library(GenomicRanges) bar <- matrix(rnorm(100), ncol=10) colnames(bar) <- as.character(1:10) rownames(bar) <- letters[1:10] foo <- SummarizedExperiment(assays=list(bar=bar)) rowData(foo) ## GRangesList object of length 10: ## $a ## GRanges object w

Re: [Bioc-devel] Help with creating first Bioconductor package

feel free to put the code up on GitHub if you want comments prior to review (e.g. "vignette won't compile", "dependencies are screwed up", "S3 objects as far as the eye can see", etc.) Statistics is the grammar of science. Karl Pearson On Fr

Re: [Bioc-devel] PPA with built bioconductor packages (for continuous integration)

agreed on Rocker and it gives me an excuse to bug Dirk. Errr, I mean, test it Statistics is the grammar of science. Karl Pearson On Mon, Nov 10, 2014 at 10:04 AM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Laurent G

Re: [Bioc-devel] PPA with built bioconductor packages (for continuous integration)

Yes. The same sort of thing happens when I send code to others. The library dependencies often take longer to install than the code takes to run, and these are not trivial analyses (thousands of cases across dozens of studies with millions to billions of data points). The idea of a PPA in a VM

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