[Bioc-devel] Whether to copy unexported BSgenome function into multicrispr

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

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

define a methods::setAs without loading the class definition? Aditya From: Michael Lawrence [lawrence.mich...@gene.com] Sent: Friday, September 06, 2019 1:09 PM To: Bhagwat, Aditya Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and o

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

I noticed the unfriendly indentation and formatting of my response , so I updated my original question on BioC support (with a much more eye-friendly formatting): https://support.bioconductor.org/p/124442 From: Bhagwat, Aditya Sent: Friday, September 06, 2019

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

el Lawrence via Bioc-devel escribió: > I'm pretty surprised that the karyoploteR package does not accept a > Seqinfo since it is plotting chromosomes. But again, please consider > just doing as(seqinfo(bsgenome), "GRanges"). > > On Wed, Sep 11, 2019 at 3:59 AM Bhagwat, A

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

>> >> Bernat >> >> >> El 9/11/19 a las 2:31 PM, Michael Lawrence via Bioc-devel escribió: >>> I'm pretty surprised that the karyoploteR package does not accept a >>> Seqinfo since it is plotting chromosomes. But again, please consider >>

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

felt not not comply to these. Thanks for all the feedback - has been very helpful. Aditya From: Pages, Herve [hpa...@fredhutch.org] Sent: Wednesday, September 11, 2019 5:29 PM To: Michael Lawrence; Bhagwat, Aditya Cc: bioc-devel@r-project.org Subject: Re

[Bioc-devel] Extending GenomicRanges::`intra-range-methods`

Dear bioc-devel, The ?GenomicRanges::`intra-range-methods` are very useful for range arithmetic Feedback request: would it be of general use to add the methods below to the

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

y there are three Vector -> data.frame coercers in S4Vectors<https://support.bioconductor.org/p/124491>) Cheers, Aditya From: Pages, Herve [hpa...@fredhutch.org] Sent: Tuesday, September 10, 2019 6:45 PM To: Bhagwat, Aditya; bioc-devel@r-p

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

esday, September 11, 2019 12:24 PM To: Bhagwat, Aditya; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)? Hi Aditya, On 9/11/19 01:31, Bhagwat, Aditya wrote: > Hi Herve, > > > > It feels that a coercion method

Re: [Bioc-devel] Collapsing a GRangesList into a GRanges without loosing names(GRangesList)

Oh, that's pretty cool :-) I knew I was overlooking something! Thanks Lori Aditya From: Shepherd, Lori [lori.sheph...@roswellpark.org] Sent: Wednesday, September 11, 2019 2:54 PM To: Bhagwat, Aditya; bioc-devel@r-project.org Subject: Re: Collapsing a GRangesList

[Bioc-devel] Collapsing a GRangesList into a GRanges without loosing names(GRangesList)

Dear bioc-devel, When using unlist to collapse a GRangesList into a GRanges one looses names(GRangesList). Since I need a name-preserving collapser, I defined the following in multicrispr. My

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

;GRanges", function(from) from %>% GenomeInfoDb::seqinfo() %>% as('GRanges')) Thankyou for feedback, Aditya From: Michael Lawrence [lawrence.mich...@gene.com] Sen

[Bioc-devel] read_bed()

Dear bioc-devel, I had two feedback requests regarding the function read_bed(). 1) Did I overlook, and therefore, re-invent existing functionality? 2) If not, would `read_bed` be suited for existence in a more foundational package, e.g. `GenomicRanges`, given the rather basal nature of this

Re: [Bioc-devel] read_bed()

Aha - thx! Aditya From: Shepherd, Lori [lori.sheph...@roswellpark.org] Sent: Tuesday, September 17, 2019 1:02 PM To: Bhagwat, Aditya; bioc-devel@r-project.org Subject: Re: read_bed() Please look at rtracklayer::import() function that we recommend for reading

Re: [Bioc-devel] read_bed()

ficially valid BED files, and as such rtracklayer does not yet support them (this will be addressed soon). Which brings the question: how soon is soon :-D ? Aditya From: Shepherd, Lori [lori.sheph...@roswellpark.org] Sent: Tuesday, September 17, 2019 1:02 PM T

Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

Owkies, will file a PR in one of the coming days. And continue the discussion when I do so. Cheers! Aditya From: Stuart Lee [le...@wehi.edu.au] Sent: Tuesday, September 17, 2019 5:33 AM To: Michael Lawrence Cc: Bhagwat, Aditya; bioc-devel@r-project.org Subject

Re: [Bioc-devel] read_bed()

...@gene.com] Sent: Tuesday, September 17, 2019 1:41 PM To: Bhagwat, Aditya Cc: Shepherd, Lori; bioc-devel@r-project.org Subject: Re: [Bioc-devel] read_bed() I don't see an attachment, nor can I find the multicrispr package anywhere. The "addressed soon" was referring to the BEDX+Y form

Re: [Bioc-devel] read_bed()

From: Michael Lawrence [lawrence.mich...@gene.com] Sent: Tuesday, September 17, 2019 2:05 PM To: Bhagwat, Aditya Cc: Michael Lawrence; Shepherd, Lori; bioc-devel@r-project.org Subject: Re: [Bioc-devel] read_bed() It breaks it because it's not standard BED; however

Re: [Bioc-devel] read_bed()

: Michael Lawrence [lawrence.mich...@gene.com] Sent: Tuesday, September 17, 2019 2:23 PM To: Bhagwat, Aditya Cc: Michael Lawrence; Shepherd, Lori; bioc-devel@r-project.org Subject: Re: [Bioc-devel] read_bed() The generic documentation does not mention it, but see ?import.bed. It's similar to colClasses

Re: [Bioc-devel] read_bed()

Oh :-) - Thankyou for explaining! From: Michael Lawrence [lawrence.mich...@gene.com] Sent: Tuesday, September 17, 2019 2:40 PM To: Bhagwat, Aditya Cc: Michael Lawrence; Shepherd, Lori; bioc-devel@r-project.org Subject: Re: [Bioc-devel] read_bed() Having

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

Waaw, thanks Michael, that is really clarifying. From: Michael Lawrence [lawrence.mich...@gene.com] Sent: Friday, September 06, 2019 7:32 PM To: Bhagwat, Aditya Cc: Kasper Daniel Hansen; Michael Lawrence; bioc-devel@r-project.org Subject: Re: [Bioc-devel

[Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

Dear Bioc devel, Is it possible to import the BSgenome class without attaching BiocGenerics (to keep a clean namespace during the development of multicrispr). BSgenome <- methods::getClassDef('BSgenome', package = 'BSgenome') (Posted

Re: [Bioc-devel] read_bed()

Thank you Michael :-) Aditya From: Michael Lawrence [lawrence.mich...@gene.com] Sent: Tuesday, September 17, 2019 8:49 PM To: Bhagwat, Aditya Cc: Michael Lawrence; bioc-devel@r-project.org Subject: Re: [Bioc-devel] read_bed() I think you probably made

Re: [Bioc-devel] read_bed()

t make sense to import/re-export import.bed() in multicrispr? What is BioC convention/best practice in such cases? Aditya From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Wednesday, Sep

Re: [Bioc-devel] read_bed()

ad.bed in multicrispr? What is BioC convention/best practice in such cases? Aditya From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Wednesday, September 18, 2019 8:35 AM To: Michael Lawre

Re: [Bioc-devel] read_bed()

] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Wednesday, September 18, 2019 1:57 PM To: Michael Lawrence Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] read_bed() Hi Michael, That's a software design dilemma I've encountered a few times. One approach is to keep

Re: [Bioc-devel] read_bed()

Actually, I will keep multicrispr::read_bed(), but wrap it around rtracklayer::import.bed, and additionally plot and print range summaries. Aditya From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi

Re: [Bioc-devel] read_bed()

and visual feedback which I intent to give. Interesting to hear your suggestions on this topic, though. Aditya From: Michael Lawrence [lawrence.mich...@gene.com] Sent: Wednesday, September 18, 2019 1:33 PM To: Bhagwat, Aditya Cc: Michael Lawrence; bioc

Re: [Bioc-devel] read_bed()

gwdg.de/loosolab/software/multicrispr/blob/master/R/03_read.R>, based on data.table::fread is doing the job, so I will stick to that . Thank you for all feedback, Cheers, Aditya From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat,

Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

) # left and right flanks What do you think? Aditya From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Monday, September 16, 2019 10:30 AM To: Michael Lawrence Cc: bioc-devel@r-project.org

Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

Hmm no that wouldn't work, it would become messy trying to figure out when incompatible arguments are provided. Aditya From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Monday

Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

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 function: straddle(x, side, left, > right,

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

LSE, ...) { x <- as.vector(x) as.data.frame(x, row.names=row.names, optional=optional, ...) }) From: Kasper Daniel Hansen Sent: Freitag, 6. September 2019 17:49 To: Michael Lawrence Cc: Bhagwat, Aditya ; bioc-devel@r-project.org Subject: R

Re: [Bioc-devel] From Biostring matching to short read mapping

Date: Fri, 8 Nov 2019 18:19:27 + From: "Pages, Herve" To: "Bhagwat, Aditya" , "bioc-devel@r-project.org" Subject: Re: [Bioc-devel] From Biostring matching to short read mapping Message-ID: <84550bd2-9ded-04a

Re: [Bioc-devel] From Biostring matching to short read mapping

Thank you Wei, I actually love Rsubread, and use it with much appreciation on RNAseq projects, thank you for its creation :-) Cheers, Aditya From: Wei Shi [s...@wehi.edu.au] Sent: Saturday, November 09, 2019 12:02 PM To: Bhagwat, Aditya; Pages, Herve; bioc

Re: [Bioc-devel] From Biostring matching to short read mapping

, November 08, 2019 7:19 PM To: Bhagwat, Aditya; bioc-devel@r-project.org Cc: Wei Shi (s...@wehi.edu.au); Michael Stadler (michael.stad...@fmi.ch) Subject: Re: From Biostring matching to short read mapping Hi Aditya, Should not be too hard to parallelize. With some gotchas: using one worker per

[Bioc-devel] From Biostring matching to short read mapping

Dear bioc-devel, 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 this is done with

[Bioc-devel] plyranges group_by

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, but that is not the topic of this email - I have been asked by Lori not to double-post :-)). This email is about

[Bioc-devel] (no subject)

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

Re: [Bioc-devel] plyranges group_by

To: Bhagwat, Aditya Cc: Stuart Lee; Michael Lawrence; bioc-devel@r-project.org Subject: Re: plyranges group_by I replied on the support site. Let's move the discussion there. On Thu, Oct 17, 2019 at 1:24 AM Bhagwat, Aditya mailto:aditya.bhag...@mpi-bn.mpg.de>> wrote: Thank you Stuart and Michael fo

Re: [Bioc-devel] plyranges group_by

ly)? I wouldn't mind writing a function to do that (in github), but first need your feedback as to whether you think that would be useful :-) Aditya From: Stuart Lee [le...@wehi.edu.au] Sent: Thursday, October 17, 2019 3:01 AM To: Michael Lawrence Cc: Bhagwat,

[Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb missing for human

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

[Bioc-devel] rtracklayer::import.bed(genome = Seqinfo)

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 second option does not work on my BED file (in

[Bioc-devel] bsapply and vcountPattern: sapply -> bplapply

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, etc operations into parallellized

[Bioc-devel] How to import a setAs method in one's package?

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]] ___

Re: [Bioc-devel] How to import a setAs method in one's package?

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

Re: [Bioc-devel] How to import a setAs method in one's package?

Thankyou guys for your quick and helpful feedback! Aditya From: Michael Lawrence [lawrence.mich...@gene.com] Sent: Friday, May 08, 2020 7:35 PM To: Bhagwat, Aditya Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] How to import a setAs method in one's

[Bioc-devel] multicrispr: builds fine on all test platforms except one (nebbiolo)

Dear BiocCore, multicrispr is building fine on all test platforms except one (nebbiolo): Could the build error be arising from some

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

ult for coercing "BSgenome" to "GenomeDescription" Aditya From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Tuesday, July 07, 2020 10:22 AM To: bioc-devel@r-project.org Sub

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Sorry, my earlier email had a copy/paste error - corrected now From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Tuesday, July 07, 2020 10:50 AM To: bioc-devel@r-project.org Subject: Re

[Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Dear bioc-devel, multicrispr is having an error on the bioc-devel build machines, caused by: unable to find an inherited method for function 'bsgenomeName' for signature '"BSgenome" This is a bit

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Thankyou Herve! I guess that means that I can pull the fix in a day or two, is that right? Aditya From: Hervé Pagès [hpa...@fredhutch.org] Sent: Tuesday, July 07, 2020 11:45 AM To: Bhagwat, Aditya; bioc-devel@r-project.org Subject: Re: [Bioc-devel

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Fantastic - thankyou Herve! Aditya From: Hervé Pagès [hpa...@fredhutch.org] Sent: Tuesday, July 07, 2020 11:55 AM To: Bhagwat, Aditya; bioc-devel@r-project.org Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel? On 7/7/20 02

[Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

Dear Bioc Core, Thank you for accepting multicrispr on BioC. I was going through the instructions on how to sync existing repositories. All instructions up to

Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

://bioconductor.org/developers/how-to/git/faq/ #14 did work for me, but the above explanation makes sense. Thanks! Aditya From: Shepherd, Lori [lori.sheph...@roswellpark.org] Sent: Thursday, June 11, 2020 6:18 PM To: Bhagwat, Aditya; bioc-devel@r-project.org

Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

[lori.sheph...@roswellpark.org] Sent: Thursday, June 11, 2020 6:18 PM To: Bhagwat, Aditya; bioc-devel@r-project.org Subject: Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it Newly accepted packages are added int

Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

Owkies, thx! Aditya From: Shepherd, Lori Sent: Freitag, 12. Juni 2020 17:42 To: Bhagwat, Aditya ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it If you git clone the git.bioconductor.org

[Bioc-devel] autonomics: warnings only on tokay2

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

[Bioc-devel] autonomics DOI link inactive

Dear bioc-devel, Thank you for having autonomics on bioc-devel. The DOI link seems to be inactive, is this normal: https://doi.org/doi:10.18129/B9.bioc.autonomics Thankyou, Aditya [[alternative HTML version deleted]]

Re: [Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb missing for human

Thankyou Lori, Cheers, Aditya From: Shepherd, Lori [lori.sheph...@roswellpark.org] Sent: Tuesday, October 15, 2019 2:22 PM To: Bhagwat, Aditya; bioc-devel@r-project.org Subject: Re: Converting gene ids to GRanges - ensembl centric TxDb missing for human Again