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Dear Michael, # This works rtracklayer::import.bed('SRF.bed', genome = 'mm10') # this works # But this doesn't seqinfo1<- GenomeInfoDb::seqinfo(BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10) rtracklayer::import.bed('SRF.bed', genome = seqinfo1) # Neither does

Dear Bioc-devel, Only on tokay2 (windows server), autonomics is giving warnings: http://bioconductor.org/spb_reports/autonomics_buildreport_20210209130019.html It looks like something strange is happening on tokay2, or have I overlooked something? Thank you for feedback! Aditya...

Dear bioc-devel, Thank you for having autonomics<https://bioconductor.org/packages/devel/bioc/html/autonomics.html> on bioc-devel. The DOI link seems to be inactive, is this normal: https://doi.org/doi:10.18129/B9.bioc.autonomics Thankyou...

Dear BioC compatriots, How does one import a setAs method (which is generally not exported)? I in particular need to import as(., DataFrame) and am a bit puzzled on how to do this. Thank you! Aditya [[alternative HTML version deleted]]

Dear Bioc devel, Is it possible to import the BSgenome class without attaching BiocGenerics (to keep a clean namespace during the development of multicrispr<https://gitlab.gwdg.de/loosolab/software/multicrispr>). BSgenome <- methods::getClassDef('BSgenome', package = 'BSgenome') (Posted earlier on...

Dear BiocCore, multicrispr <https://bioconductor.org/packages/devel/bioc/html/multicrispr.html> is building fine on all test platforms except one (nebbiolo<http://bioconductor.org/checkResults/devel/bioc-LATEST/multicrispr/nebbiolo1-buildsrc.html>): Could the build error be arising from...

Dear Herve & co, Wish you a happy new year :-). I am optimizing code that calls BSgenome::vcountPDict. BSgenome::vcountPDict calls bsapply, which calls sapply. Could this sapply be replaced by a bplapply instead - that would turn all the vcount, vmatch...

Dear Michael, Sorry for my incomplete email - the send button got hit too fast. Better this time. rtracklayer::import.bed mentions the argument "genome" to be either a genome identifier (like 'mm10') or a Seqinfo object. I notice that the...

Dear bioc-devel, multicrispr is having an error on the bioc-devel build machines<https://bioconductor.org/checkResults/3.12/bioc-LATEST/multicrispr/malbec1-checksrc.html>, caused by: unable to find an inherited method for function 'bsgenomeName' for signature '"BSgenome...

Dear bioc-devel, I recently changed institutes and, hence, email address (from @mpi-bn to @uni-marburg). Following the advice in this post<https://stat.ethz.ch/pipermail/bioc-devel/2021-February/017697.html>, I updated: * Bioc-devel mailing list...

Looks like this can be successfully done by @importFrom methods as @importFrom S4Vectors DataFrame Cheers, Aditya ________________________________________ From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Bhagwat, Aditya [Aditya.Bhagwat at mpi-bn.mpg.de] Sent: Friday...

Dear Bioc Core, Thank you for accepting multicrispr on BioC<https://github.com/Bioconductor/Contributions/issues/1486>. I was going through the instructions on how to sync existing repositories<https://bioconductor.org/developers/how-to/git/sync-existing-repositories/>. All...

Dear bioc-devel, When using unlist to collapse a GRangesList into a GRanges<https://support.bioconductor.org/p/83599> one looses names(GRangesList). Since I need a name-preserving collapser, I defined the following in multicrispr<https://gitlab.gwdg.de...

Dear BioC devel, I want to convert geneids to GRanges by doing: GenomicFeatures::genes(txdb)[geneids] Works wonderfully for mouse, with entrezgene as well ensemblgene-centric TxDbs: txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene::TxDb.Mmusculus.UCSC.mm10.knownGene GenomicFeatures::genes...

Dear bioc-devel, multicrispr<https://gitlab.gwdg.de/loosolab/software/multicrispr> provides functions for Crispr/Cas9 gRNA design (and is being prepared for BioC). One task involves finding all genomic (mis)matches of a 23-bp candidate Cas9 sequence. Currently...

Dear BioC developers, BSgenome::getBSgenome('mm10') returns BSgenome.Mmusculus.UCSC.mm10::Mmusculus. But that function also attaches BiocGenerics, S4Vectors, IRanges and Biostrings, which is unfortunate from a keep-the-namespace-clean perspective. I could instead use the clean alternative bsname...

Thanks Michael, The important detail is that I want to plot the relevant chromosomes only relevant_chromosomes <- GenomeInfoDb::seqnames(grangeslist) %>% S4Vectors::runValue() %>% Reduce(union, .) %>% unique() genomeranges <- GenomeInfoDb::seqinfo(grangeslist) %>% as('GRanges') %>% (function(gr){ gr [ as.character(GenomeInfoDb::seqnames(gr)) %in...

Hi Michael, Thank you for the pointer to plyranges - looks very useful! > Maybe a better name is "straddle" for when ranges > straddle one of the endpoints? In keeping with the current pattern of > Ranges API, there would be a single...

Hi Stuart, Michael, Your plyranges package is really cool - now I am using it for left joining GRanges (I am facing a minor issue there<https://support.bioconductor.org/p/125623/>, but that is not the topic of this email...

Thankyou guys for your quick and helpful feedback! Aditya ________________________________________ From: Michael Lawrence [lawrence.michael at gene.com] Sent: Friday, May 08, 2020 7:35 PM To: Bhagwat, Aditya Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] How...