Re: [Bioc-devel] Unable to install Bioconductor despite multiple attempts and troubleshooting

Hi, Chiagozie. This list is mainly for developer questions. Your best bet is to ask on https://support.bioconductor.org/ where you'll get many more eyes on your question and the broadest possible community will benefit from answers. When you ask there, consider adding the output of sessionInfo()

Re: [Bioc-devel] Split by function for plotdots

Hi, Amin. You�ll have a more likely chance of an answer if you post to the Bioconductor support site at https://support.bioconductor.org. This list is really focused to development-related issues. Best, Sean From: Bioc-devel on behalf of Amin Ali Date: Monday, October 31, 2022 at 5:18 AM

Re: [Bioc-devel] Mac ARM64 binaries available

My sentiments exactly! Great work! Sean From: Bioc-devel on behalf of Steve Lianoglou Date: Tuesday, September 27, 2022 at 1:25 PM To: Jennifer Wokaty Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Mac ARM64 binaries available a yeah thanks for the hard work,

Re: [Bioc-devel] Merging or renaming a fork, and appropriate journal for package updates

Hi, Pariksheet. For #1, I suspect that it might be challenging to publish a paper based on the context you provide, but I do not have a good handle on the specific changes you have proposed. To make your work publishable, you would probably need to at least publish the software and it appears

Re: [Bioc-devel] FW: Biconductor package ANCOMBC

Hi, Huang. It looks like you might need to add the rmarkdown package in Suggests (and version bump to catch the change): http://bioconductor.org/checkResults/devel/bioc-LATEST/ANCOMBC/nebbiolo2-buildsrc.html Since the windows binary version is building, I'm guessing that may fix the issue.

Re: [Bioc-devel] Vignette examples

-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twitter.com/seandavis12 [[alternative HTML ver

Re: [Bioc-devel] bioconductor_docker updates

> >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > > > > -- > > > > Levi Waldron > > > > Associate Professor > > > > Department of Epidemiology and Biosta

Re: [Bioc-devel] d3heatmap dependency error

without > d3heatmap? Or is there an easy alternative to d3heatmap? > > Thanks, > Mani > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Se

Re: [Bioc-devel] Reducing dependencies

some larger packages from ‘Imports’ to > ‘Suggests’, but to no avail. > > Best, > Koen > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bio

Re: [Bioc-devel] Images from vignettes

; > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Be

Re: [Bioc-devel] Deploy a critical patch

On Tue, Mar 17, 2020 at 11:48 PM Julian Flesch wrote: > Hi Bioc team, > > > I am the maintainer of the package /waddR/. > > We have had built issues on the active branch recently, due a dependency > being unavailable. After pushing a patch, the issues were resolved on > the devel branch. > > Is

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

There are some good ideas here that would provide enhancement to BiocPkgTools. I don't have the bandwidth to incorporate right now, but filing issues or a pull request with a skeleton would be helpful to keep track. Sean On Sun, Feb 9, 2020 at 7:31 AM Vincent Carey wrote: > On Sat, Feb 8, 2020

Re: [Bioc-devel] Bioconductor 3.10 is released!!

ernative HTML version deleted]] > > _______ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Heal

Re: [Bioc-devel] download statistics for 2019?

ited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org ma

Re: [Bioc-devel] Canceled event: Biocondutor Developers Forum @ Thu Aug 15, 2019 12pm - 1pm (EDT) (bioc-devel@r-project.org)

ecipient to send a response > to > > the organizer and be added to the guest list, or invite others regardless > > of their own invitation status, or to modify your RSVP. Learn more at > > https://support.google.com/calendar/answer/37135#forwarding > > ___

Re: [Bioc-devel] Problem downloading files with GenomicDataCommons

utational Genomics Group, > IFOM - The FIRC Institute of Molecular Oncology, > Via Adamello 16, > 20139 Milano, Italy. > Phone: +393441130157 > E-mail: koustav@ifom.eu > > > > > [[alternative HTML version deleted]] > > __

Re: [Bioc-devel] InteractionSet for structural variants

On Tue, May 21, 2019 at 2:54 AM Aaron Lun < infinite.monkeys.with.keyboa...@gmail.com> wrote: > > Thanks for your response. So far my intention is to to plot them and I > > do not intend on performing any other operation. The first step would be > > read in the VCF file and transform it into a

[Bioc-devel] Behavior of BiocManager::install() with github repos on Mac

s://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/GEOquery_2.51.5.tgz ' Content type 'application/x-gzip' length 13828923 bytes (13.2 MB) == downloaded 13.2 MB -- Sean Davis, MD, PhD Center for Cancer Research National Cancer

Re: [Bioc-devel] Using https to maintain a package

; [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute Nat

Re: [Bioc-devel] DOI information

ML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Beth

Re: [Bioc-devel] Subsetting Multiple platform build/check report

__ > > > Bioc-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > [[alternative HTML version deleted]] > > > > ___

[Bioc-devel] Call for papers for Bioconductor F1000Research Gateway

work. Thanks, Sean (on behalf of the F1000Research Bioconductor Advisory Board) -- -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twitter.com/seandavis12 [[alternative HTML

Re: [Bioc-devel] hail and bioc

I'd be interested to see one. I don't think it has been done yet. On Fri, Feb 23, 2018 at 9:19 AM Michael Lawrence wrote: > Has anyone made a bioc interface to Hail yet? If not I might try to make > one, just for fun. > > Michael > > [[alternative HTML version

Re: [Bioc-devel] Bioconductor says I am not subscribed to bioc-devel

r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twit

[Bioc-devel] Fwd: [SIAM-LS] New NSF funding opportunity: Rules of Life (RoL): Forecasting and Emergence in Living Systems

This new NSF funding opportunity might interest a few folks on this list. Sean -- Forwarded message -- Subject: [SIAM-LS] New NSF funding opportunity: Rules of Life (RoL): Forecasting and Emergence in Living Systems Dear Colleagues: NSF seeks to highlight the importance of

Re: [Bioc-devel] Data package timeouts

9] limma_3.34.2 xml2_1.1.1 readr_1.1.1 glue_1.2.0 > [13] purrr_0.2.4 hms_0.4.0compiler_3.4.2 pkgconfig_2.0.1 > [17] bindr_0.1tibble_1.3.4 > > > On Thu, Nov 30, 2017 at 11:56 AM, Leonardo Collado Torres > <lcoll...@jhu.edu> wrote: > >

Re: [Bioc-devel] BiocFileCache for developers

3 > ------ > *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Sean > Davis <seand...@gmail.com> > *Sent:* Friday, December 1, 2017 11:06:39 AM > *To:* Michael Love > *Cc:* bioc-devel@r-project.org > *Subject:* Re: [Bioc-deve

Re: [Bioc-devel] BiocFileCache for developers

The default user_cache_dir may not be the best choice there. Sean > > thanks, > Mike > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Sean Davis, MD, PhD Cent

Re: [Bioc-devel] Build failing for MutationalPatterns

On Thu, Nov 30, 2017 at 10:01 AM, Janssen-10, R.R.E. < r.r.e.janssen...@umcutrecht.nl> wrote: > Dear Martin, > > Martin writes: > > > On 11/29/2017 11:14 AM, Janssen-10, R.R.E. wrote: > >> Hi Martin, > >> > >> Thanks for your reply! > >> > >> Martin Morgan writes: > >> > >>> On 11/29/2017 09:58

Re: [Bioc-devel] Data package timeouts

; On 30 November 2017 at 11:20, Sean Davis <seand...@gmail.com> wrote: > >> Thanks for the report, Mike. >> >> The problem was (specifically) in parsing a GSEMatrix file using a >> filename. This should be fixed in versions 2.46.10 (release) and 2.47.12 >> (de

Re: [Bioc-devel] Data package timeouts

___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://s

Re: [Bioc-devel] Bioconductor build reports as a tidy data frame

orresponding glyph status? :-P > I leave that as an exercise for the reader. ; ) Sean > > Thanks, > H. > > > On 11/17/2017 12:16 PM, Sean Davis wrote: > >> Just in case some developers would like to review the Bioconductor build >> report as computabl

[Bioc-devel] Bioconductor build reports as a tidy data frame

Just in case some developers would like to review the Bioconductor build report as computable data in R: http://bit.ly/2zKL3M3 Sean -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https

Re: [Bioc-devel] rcellminer Bioconductor package

and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received

Re: [Bioc-devel] joining community-bioc slack

el. > > Thanks > Nate > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Sean Davis, MD, PhD Center for Cancer Research National Canc

Re: [Bioc-devel] git clone failed from git.bioconductor.org

___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github

Re: [Bioc-devel] Moving from development build to release build

r.org/packages/devel/bioc/html/oneSENSE.html > > > -- > Best Wishes, > Tan Yong Kee > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel &

Re: [Bioc-devel] COHCAP GitHub Update

col is not machine-type dependent, although how to use ssh keys may vary a bit, particularly on windows. Sean > > ~/.ssh$ ssh -T g...@git.bioconductor.org > Permission denied (publickey). > > Thanks, > Charles > > > > On Mon, Sep 4, 2017 at 5:28 PM, Sean Davis

Re: [Bioc-devel] updating Bioconductor package that is already on Github

; Washington, DC 20007 > Phone: (202) 687-1545 > Fax: (202) 687-5011 > http://icbi.georgetown.edu/boca > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/

Re: [Bioc-devel] COHCAP GitHub Update

(typo in the URL, missing or mismatched ssh key) were overcome already. I'd proceed from there. Hope that helps, Sean > > Thanks, > Charles > > On Mon, Sep 4, 2017 at 11:41 AM, Sean Davis <seand...@gmail.com> wrote: > >> Hi, Charles. >> >> The command

Re: [Bioc-devel] COHCAP GitHub Update

it/sync- > > existing-repositories/ > > > > > > However, if I run the command *git remote add upstream > > > g...@git.bioconductor.org:packages/COHCAP.gi**t*, then I get an error > > > message: *fatal: Not a git repository.* > > > > > > &g

Re: [Bioc-devel] Problems with updating release branch

formation is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org maili

Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org

l Brumme-Bothe > > Geschäftsführer: Prof. Dr. Günther Wess, Heinrich Baßler, Dr. Alfons > Enhsen > > Registergericht: Amtsgericht München HRB 6466 > > USt-IdNr: DE 129521671 > > > > This email message may contain legally p

Re: [Bioc-devel] Bioconductor stats

ats. > Again, mirrors are not included. I think the distinct IPs are reset per month for the monthly stats. > > Regards, > > Lluís > > [[alternative HTML version deleted]] > > _______ > Bioc-devel@r-project.org mailing list > h

Re: [Bioc-devel] DMRcate: TIMEOUT

cs and Epigenetics Division > > Garvan Institute of Medical Research > > 384 Victoria St., Darlinghurst, NSW, Australia 2010 > > Tel: +61 (2) 9295 8319 > > > [[alternative HTML version deleted]] > > ___ > Bioc-deve

Re: [Bioc-devel] Error trying to update remotes

tions? >> >> Thank you >> >> Greg Gloor >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > > This email message may contain legally privile

Re: [Bioc-devel] Vignette update after change in git mirror repo

Sorry I lead you astray, earlier, Maia. In general, you do not need to install the package in the vignette. The first code block in the vignette where you did "eval=FALSE" is the way to go. The second code block where you actually do the installation is unnecessary. The package is installed by R

Re: [Bioc-devel] Vignette update after change in git mirror repo

ml). Perhaps I made an error > somewhere? > > Best, > Maia > > On Thu, Apr 20, 2017 at 1:24 PM, Sean Davis <seand...@gmail.com> wrote: > >> Hi, Maia. >> >> The git mirror is not used for building packages. Instead, you will need >> to commit to svn f

Re: [Bioc-devel] Vignette update after change in git mirror repo

Hi, Maia. The git mirror is not used for building packages. Instead, you will need to commit to svn for changes to show up on Bioconductor. See here for details of working with git and svn together. https://www.bioconductor.org/developers/how-to/git-mirrors/ If I misunderstood what you are

Re: [Bioc-devel] Question about R functions

gt; >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> ___ >>> Bioc-devel@r-project.org mailing list >>> https://stat.eth

Re: [Bioc-devel] Writing examples for accessing web API

Hi, Welliton. Great question. Just out of curiosity, what are the internet connection requirements that preclude running examples? Is authentication required? Or are you connecting to a server that runs only intermittently? Sean On Tue, Mar 7, 2017 at 1:57 PM, Welliton Souza

[Bioc-devel] Naming and namespace collisions for commonly-named functions

Hi, all. I am curious about what folks think about naming conventions for commonly named functions, some of which are so common that even establishing a generic would be difficult because of different use cases. Examples include things like “filter”. One possibility is to use the Google Sheets

Re: [Bioc-devel] Package reference manuals in html

Github allows you to set the branch for the docs directory if I recall. Perhaps a separate branch with a docs directory (not master) is a viable way to go? Sean > On Dec 23, 2016, at 12:16 PM, Laurent Gatto wrote: > > > There's actually another side-effect for

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

> On Nov 30, 2016, at 4:13 PM, Martin Morgan > wrote: > > On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote: >> Full transcript please; you're compiling from source. > > Excuse my ignorance about the Mac world but shouldn't these be available for > binary

Re: [Bioc-devel] No Significant hits!

Hi, Pabita. This question is better asked on the bioconductor support site ( HTTPS://support.bioconductor.org). However, finding no evidence for differential expression is not uncommon. Whether it is expected or not is hard to comment on without data. Sean On Jul 30, 2016 10:43, "Pabita Basnet"

Re: [Bioc-devel] GEOquery for Bioc devel

Hi, all. Sorry for the hiccup. The problem appears to have stemmed from NCBI GEO switching to using https for GEO data tables. This is not a highly-used feature, but it was enough to break the build. It should be fixed (cross fingers) in Devel. If fixed in devel, I will backport to

[Bioc-devel] Creating Biostrings DNAStringSet from Rcpp/C++

Forgive the really naive questions, but my C/C++ and Biostrings skills are pretty rough. I have been playing with Rcpp to interface to an external library for reading sequence formats. I am reading DNA sequences one-at-a-time and would like to package a set of those up as a DNAStringSet. I

Re: [Bioc-devel] Removed packages and package landing pages

/bioc_3_1_release/ . That's a bit hands-on, as you sometimes have to go back several releases to see when it got removed, so hopefully Dan has a more reasonable approach. Jim On Thu, Aug 6, 2015 at 6:35 AM, Sean Davis seand...@gmail.com wrote: Hi, Dan. A user asked me a question about the DnaseR

[Bioc-devel] Removed packages and package landing pages

Hi, Dan. A user asked me a question about the DnaseR package. It appears to have been removed from Bioc? Where would I find that out? What is the behavior of the release/devel pages if a package has been previously removed? Thanks, Sean [[alternative HTML version deleted]]

Re: [Bioc-devel] vignettes with different builders in one package?

Hi, Vince. It seems like knitr should be able to build a sweave vignette, particularly if the stuff in the has been converted from sweave to knitr format? It might be easier to do that than to convert the original to Rmarkdown. Sean On Mon, Aug 3, 2015 at 6:57 PM, Vincent Carey

Re: [Bioc-devel] csaw - suggestions

Hi, Arne. This question is best posted on the support site: https://support.bioconductor.org/ To give a preview of the answer, though, while coverage and binned counts are related concepts, they are not really identical. The csaw package is looking for read counts. Sean On Tue, Jul 7, 2015

[Bioc-devel] Just for fun

The last Bioconductor development cycle visualized as a graph using gource is available here: https://youtu.be/-HZ4XOh49fw Sean [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list

Re: [Bioc-devel] Use of confounders in downstream analysis

Hi, Aileen. This list isn't really the best place to ask questions like this and is really reserved for discussion around package development. Could you please post to: https://support.bioconductor.org/ That way, you benefit from more eyes and everyone benefits from potential answers. Thanks,

Re: [Bioc-devel] Docker granularity: containers for individual R packages, running on a normal R installation?

Hi, Wolfgang. One way to think of docker is as a very efficient, self-contained virtual machine. The operative term is self-contained. The docker containers resemble real machines from the inside and the outside. These machines can expose ports and can mount file systems, but something like

Re: [Bioc-devel] request for more notices about build issues

Is this a use case for a graphical build report that displays the build status on a graph/DAG? http://www.bioconductor.org/packages/release/bioc/vignettes/pkgDepTools/inst/doc/pkgDepTools.pdf pkgDepTools, combined with a computable build report (a downloadable version of the current build

Re: [Bioc-devel] A quick check for matching seqnames/order needed for Views on RleList?

the Views method has to handle that, and in my opinion return it in the order of cds list in this case. Anything else is way too fragile. On Fri, Feb 20, 2015 at 8:14 AM, Sean Davis seand...@gmail.com wrote: On Fri, Feb 20, 2015 at 8:10 AM, Malcolm Perry mgperr...@gmail.com wrote: Hi Sean

Re: [Bioc-devel] A quick check for matching seqnames/order needed for Views on RleList?

that works but is nonsensical. I simply want to protect myself from making the same mistake twice by some checking inside the Views() method. Sean Hope this helps, Malcolm On Fri, Feb 20, 2015 at 12:53 PM, Sean Davis seand...@gmail.com wrote: I am calculating coverage metrics of a BAM

[Bioc-devel] A quick check for matching seqnames/order needed for Views on RleList?

I am calculating coverage metrics of a BAM file on the CDS regions. When I form the RangesList and do coverage(), the resulting coverage vector applies the views to the regions from the RangesList without checking on matching ordering or seqlevels of the RleList and the RangesList. This results,

[Bioc-devel] bamFlagAsBitMatrix error (?bug)

Hi, Martin, Val, and Herve. This looks like a little problem with the bitnames in Rsamtools/GenomicAlignments. Perhaps this is related to some bitnames being deprecated? Thanks, Sean library(GenomicAlignments) sbp = ScanBamParam(which=cds[1:100],flag=scanBamFlag(isDuplicate = FALSE)) x =

Re: [Bioc-devel] faster gene id conversion?

On Sat, Nov 22, 2014 at 12:53 AM, Karl Stamm karl.st...@gmail.com wrote: Question regarding gene name conversions. Once upon a time, I was doing a lot of gene name conversions, particularly from NM_ to HGNC symbol or Entrez GeneID. I used bioMaRt successfully, and developed a cache matrix

Re: [Bioc-devel] getting a listing of all src packages

Hi, Darin. You might find these instructions useful: http://www.bioconductor.org/about/mirrors/mirror-how-to/ Basically, you can use rsync to get the repository and keep it up-to-date. Sean On Thu, Oct 30, 2014 at 9:17 AM, Darin Perusich da...@darins.net wrote: Hello All, Would it be

[Bioc-devel] Request for Comments on The NIH Software Discovery Index--a system for linking software, publications and users in the research community

On behalf of a number of software developers, end-users, publishers associated with the scientific analysis community, we would like to invite all of you to review a document generated as a result of a NIH BD2K supported meeting that focused on the opportunities and challenges of developing a

Re: [Bioc-devel] 'semantically rich' subsetting of SummarizedExperiments

Hi, Vince. I'm coming a little late to the party, but I agree with Kasper's sentiment that the less magical approach of using subsetByXXX might be the cleaner way to go for the time being. Sean On Sat, Sep 20, 2014 at 10:42 AM, Vincent Carey st...@channing.harvard.edu wrote:

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Hi, Vince. Looks like a good start. I'd probably pull all the assays from ExpressionSet into SummarizedExperiment as the default, avoiding data coercion methods that are unnecessarily lossy. Also, as it stands, the assayname argument is not used anyway? Sean On Sat, Sep 20, 2014 at 10:38 AM,

Re: [Bioc-devel] 'semantically rich' subsetting of SummarizedExperiments

with Sean, having tried implementing to magical alternative --t On Sep 20, 2014, at 9:31 AM, Sean Davis sdav...@mail.nih.gov wrote: Hi, Vince. I'm coming a little late to the party, but I agree with Kasper's sentiment that the less magical approach of using

[Bioc-devel] [JOB] NIH-Wide Stadtman Tenure-Track Recruitment

The National Institutes of Health is now accepting applications for tenure-track positions through the Earl Stadtman recruitment mechanism. Details are available here: http://goo.gl/vF95Pi Sean [[alternative HTML version deleted]] ___

[Bioc-devel] Fwd: [JOB] NIH-Wide Stadtman Tenure-Track Recruitment

The National Institutes of Health is now accepting applications for tenure-track positions through the Earl Stadtman recruitment mechanism. Details are available here: http://goo.gl/vF95Pi Sean [[alternative HTML version deleted]] ___

Re: [Bioc-devel] Issue tracker for Bioconductor

Hi, Arun. There is not such a system that covers the entire Bioconductor project. Since packages are largely contributed by diverse developers, there are many disparate bug tracking systems in use (and many packages with no formal bug tracking). There is a facility in R to allow package authors

Re: [Bioc-devel] Question about inserting bibliographic references in a package vignette

Check in svn for the sources. Sean On Aug 8, 2014 8:58 AM, Kevin Rue-Albrecht kevin@ucdconnect.ie wrote: Hi, Thank you for your replying. Thanks Kasper, I had looked at other vignettes, but in the packages I looked at so far I only found the PDF end-result. (e.g. edgeR), or the

Re: [Bioc-devel] Bug tracker for Bioconductor?

On Fri, May 23, 2014 at 4:34 PM, Michael Lawrence lawrence.mich...@gene.com wrote: I like the idea about extracting important environmental information. Possibly the function that browses to the bug tracker could print out the sessionInfo for copy/paste. It is tempting to push the automation

Re: [Bioc-devel] WISH: BioC URL shortcut to packages

On Mon, Feb 24, 2014 at 2:22 AM, Hervé Pagès hpa...@fhcrc.org wrote: Hi, On 02/23/2014 03:58 AM, Sean Davis wrote: On Sun, Feb 23, 2014 at 12:32 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Analogously to CRAN URL shortcuts, e.g. http://cran.r-project.org/package=digest

Re: [Bioc-devel] WISH: BioC URL shortcut to packages

On Sun, Feb 23, 2014 at 12:32 AM, Henrik Bengtsson h...@biostat.ucsf.eduwrote: Analogously to CRAN URL shortcuts, e.g. http://cran.r-project.org/package=digest expanding to http://cran.r-project.org/web/packages/digest/index.html, it would be neat if Bioconductor would support

Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available

I doubt this is possible given the atomic nature of a git repository. You might look at using a second git repository and including the minfi package as a git submodule of that second repository. Then, you can keep things in sync, but the minfi repository remains atomic. Sean On Feb 21, 2014

Re: [Bioc-devel] Include indel counts in applyPileups

: Hi Sean, You can have a look at the 'bam2R' function from the 'deepSNV' package. This will extract the base/insertion/deletion counts, base call qualities, and other metrics strand-specific from a BAM file. Best wishes Julian On 13/02/14 17:09, Sean Davis wrote: Hi

[Bioc-devel] Include indel counts in applyPileups

Hi, Martin. How difficult would it be to include insertions/deletions in seq and qual in the applyPileups method for PileupFiles? The use case is to look at the context around variants for increases mismatch rates. Indels will have a small impact on such calculations, but for completeness it

Re: [Bioc-devel] Include indel counts in applyPileups

On Thu, Feb 13, 2014 at 1:12 PM, Martin Morgan mtmor...@fhcrc.org wrote: On 02/13/2014 08:09 AM, Sean Davis wrote: Hi, Martin. How difficult would it be to include insertions/deletions in seq and qual in the applyPileups method for PileupFiles? The use case is to look at the context

Re: [Bioc-devel] Memory use and coverage from BamFile

operation would be useful. Michael On Wed, Feb 12, 2014 at 1:53 AM, Sean Davis sdav...@mail.nih.gov wrote: It seems that the coverage method for BamFile() reads the entire BAM file into memory and then calls coverage. Is there a coverage method for BamFiles that does not read the entire

Re: [Bioc-devel] org-mode vignettes

This isn't a direct answer to the question, but I recently learned of this project: http://www.dexy.it/ Basically, it is a giant set of filters that runs on text-based files (MANY formats, including org) to produce outputs (MANY formats). These filters include programming languages (including R)

[Bioc-devel] FYI--Input on Development and Analysis Methods and Software for Big Data

A little off-topic, I know NHGRI has released a new RFI. There are a number of folks on this list that may have input they want to share, so I am forwarding along the Notice: http://grants.nih.gov/grants/guide/notice-files/NOT-HG-13-014.html Sean

Re: [Bioc-devel] best practice: verbose messages

On Thu, Jul 11, 2013 at 11:01 AM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: On Thu, Jul 11, 2013 at 9:57 AM, Henrik Bengtsson h...@biostat.ucsf.eduwrote: On Wed, Jul 10, 2013 at 9:10 PM, Hervé Pagès hpa...@fhcrc.org wrote: Hi Kasper, On 07/10/2013 10:50 AM, Kasper

Re: [Bioc-devel] Bioconductor coding standards

On Tue, Mar 26, 2013 at 7:27 AM, Ulrich Bodenhofer bodenho...@bioinf.jku.at wrote: On 03/26/2013 12:18 PM, Laurent Gatto wrote: On 26 March 2013 09:26, Ulrich Bodenhofer bodenho...@bioinf.jku.at wrote: Dear colleagues, One of my students is currently working on a package that we plan to

Re: [Bioc-devel] Is it possible to trigger a new build for a package on george2/moscato2/petty ?

On Wed, Jan 23, 2013 at 1:41 PM, Frederic Fournier frederic.bioi...@gmail.com wrote: Hello everyone, I recently submitted a package to bioconductor, and couple of days ago, the package started to fail the automated daily build on george2 and moscato2. Today I made some changes that work on my