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Bioc-devel October 2014

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Andrzej Oleś

Last active: Oct 3, 2014
2 msgs
Andrzej Oleś Add a new developer/maintainer Oct 3, 2014 Andrzej Oleś RMarkdown for vignettes Oct 3, 2014

Arora, Sonali

Last active: Oct 24, 2014
4 msgs
Arora, Sonali Whom to contact for adding an organism to GenomeInfoDb? Oct 22, 2014 Arora, Sonali A more flexible GenomeInfoDb::mapSeqlevels(): used supported info but don't break with new organisms/toy examples Oct 22, 2014 Arora, Sonali A more flexible GenomeInfoDb::mapSeqlevels(): used supported info but don't break with new organisms/toy examples Oct 24, 2014 Arora, Sonali Whom to contact for adding an organism to GenomeInfoDb? Oct 24, 2014

Dan Gatti

Last active: Oct 1, 2014
1 msg
Dan Gatti Rsamtools: applyPileups seg fault (!!) Oct 1, 2014

Dan Tenenbaum

Last active: Oct 31, 2014
33 msgs
Dan Tenenbaum RMarkdown for vignettes Oct 3, 2014 Dan Tenenbaum Add a new developer/maintainer Oct 3, 2014 Dan Tenenbaum Rmarkdown built html vignette not included in final package tarball Oct 6, 2014 Dan Tenenbaum Rmarkdown built html vignette not included in final package tarball Oct 6, 2014 Dan Tenenbaum odd vignette dependency issue Oct 6, 2014 Dan Tenenbaum Rmarkdown built html vignette not included in final package tarball Oct 6, 2014 Dan Tenenbaum Rmarkdown built html vignette not included in final package tarball Oct 6, 2014 Dan Tenenbaum RMarkdown for vignettes (builder issues) Oct 7, 2014 Dan Tenenbaum Updating package NEWS files for Bioconductor 3.0 release announcement Oct 8, 2014 Dan Tenenbaum Keep the bioc-help email list running? Oct 8, 2014 Dan Tenenbaum package ‘FEM’ is not available (for R version 3.0.2) Oct 9, 2014 Dan Tenenbaum no more commits allowed before release ? Oct 10, 2014 Dan Tenenbaum no more commits allowed before release ? Oct 10, 2014 Dan Tenenbaum runnable examples for internal function ? Oct 13, 2014 Dan Tenenbaum Important: Bioconductor 3.0 branch to be created today - do not commit during this time Oct 13, 2014 Dan Tenenbaum BioC 3.0 branch created Oct 13, 2014 Dan Tenenbaum Git-svn bridge for BioC 3.0 Oct 14, 2014 Dan Tenenbaum Bioconductor 3.0 is released! Oct 14, 2014 Dan Tenenbaum Bioonductor package tracker has moved Oct 15, 2014 Dan Tenenbaum Bioonductor package tracker has moved Oct 15, 2014 Dan Tenenbaum Bioonductor package tracker has moved Oct 15, 2014 Dan Tenenbaum "'BiocInstaller' package not in repository" error during nightly build Oct 16, 2014 Dan Tenenbaum "'BiocInstaller' package not in repository" error during nightly build Oct 16, 2014 Dan Tenenbaum runnable examples for internal function ? Oct 16, 2014 Dan Tenenbaum error about Display environment/ biomart for the build of my package Oct 16, 2014 Dan Tenenbaum Link posting guide in support forum Oct 17, 2014 Dan Tenenbaum Important news about pending updates to the RSQLite package Oct 20, 2014 Dan Tenenbaum Cant sign up on support site! Oct 22, 2014 Dan Tenenbaum Documentation on how to update a BioC experimental package? Oct 23, 2014 Dan Tenenbaum R-devel update schedule/strategy for Bioc devel build machines Oct 30, 2014 Dan Tenenbaum experiment data package versioning Oct 30, 2014 Dan Tenenbaum experiment data package versioning Oct 30, 2014 Dan Tenenbaum R-devel update schedule/strategy for Bioc devel build machines Oct 31, 2014

Daniel Schmolze

Last active: Oct 6, 2014
1 msg
Daniel Schmolze odd vignette dependency issue Oct 6, 2014

Darin Perusich

Last active: Oct 30, 2014
1 msg
Darin Perusich getting a listing of all src packages Oct 30, 2014

Dario Strbenac

Last active: Oct 7, 2014
3 msgs
Dario Strbenac Installing Development Version of Repitools Sep 30, 2014 Dario Strbenac Installing Development Version of Repitools Oct 1, 2014 Dario Strbenac NAMESPACE question Oct 7, 2014

Davide Risso

Last active: Oct 20, 2014
2 msgs
Davide Risso plotPCA for BiocGenerics Oct 20, 2014 Davide Risso plotPCA for BiocGenerics Oct 20, 2014

Federico Marini

Last active: Oct 15, 2014
1 msg
Federico Marini New package available: flowcatchR! Oct 15, 2014

Felix Klein

Last active: Oct 22, 2014
1 msg
Felix Klein Cant sign up on support site! Oct 22, 2014

Gabriel Becker

Last active: Oct 30, 2014
1 msg
Gabriel Becker R-devel update schedule/strategy for Bioc devel build machines Oct 30, 2014

Gordon Ball

Last active: Oct 7, 2014
2 msgs
Gordon Ball RMarkdown for vignettes Oct 3, 2014 Gordon Ball RMarkdown for vignettes (builder issues) Oct 7, 2014

Hahne, Florian

Last active: Oct 13, 2014
1 msg
Hahne, Florian Non-ASCII in datase from Biomart EMBL via Gviz package Oct 13, 2014

Henrik Bengtsson

Last active: Oct 30, 2014
9 msgs
Henrik Bengtsson RMarkdown for vignettes Oct 3, 2014 Henrik Bengtsson BiocStyle on windows with spaces in path names Oct 6, 2014 Henrik Bengtsson BiocStyle on windows with spaces in path names Oct 6, 2014 Henrik Bengtsson BiocStyle on windows with spaces in path names Oct 6, 2014 Henrik Bengtsson BiocStyle on windows with spaces in path names Oct 8, 2014 Henrik Bengtsson BiocStyle on windows with spaces in path names Oct 9, 2014 Henrik Bengtsson Documentation on how to update a BioC experimental package? Oct 23, 2014 Henrik Bengtsson depends on packages providing classes Oct 29, 2014 Henrik Bengtsson experiment data package versioning Oct 30, 2014

Hervé Pagès

Last active: Oct 30, 2014
21 msgs
Hervé Pagès minor suggestion for BiocStyle? Oct 2, 2014 Hervé Pagès Error running table() on an RleList returned by coverage() Oct 6, 2014 Hervé Pagès S4Vectors unit tests Oct 7, 2014 Hervé Pagès NAMESPACE question Oct 9, 2014 Hervé Pagès a warning we may not need any more? Oct 9, 2014 Hervé Pagès package ‘FEM’ is not available (for R version 3.0.2) Oct 9, 2014 Hervé Pagès warning when merging disjoint sets of seqlevels Oct 12, 2014 Hervé Pagès warning when merging disjoint sets of seqlevels Oct 13, 2014 Hervé Pagès runnable examples for internal function ? Oct 13, 2014 Hervé Pagès 'semantically rich' subsetting of SummarizedExperiments Oct 13, 2014 Hervé Pagès runnable examples for internal function ? Oct 16, 2014 Hervé Pagès Why be default 'D' is not dropped from coverage? Oct 20, 2014 Hervé Pagès check warning of QUALIFIER package Oct 23, 2014 Hervé Pagès Documentation on how to update a BioC experimental package? Oct 23, 2014 Hervé Pagès VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem Oct 24, 2014 Hervé Pagès depends on packages providing classes Oct 28, 2014 Hervé Pagès depends on packages providing classes Oct 28, 2014 Hervé Pagès depends on packages providing classes Oct 29, 2014 Hervé Pagès depends on packages providing classes Oct 29, 2014 Hervé Pagès getting a listing of all src packages Oct 30, 2014 Hervé Pagès experiment data package versioning Oct 30, 2014

James W. MacDonald

Last active: Oct 28, 2014
3 msgs
James W. MacDonald RMarkdown for vignettes Oct 3, 2014 James W. MacDonald BiocStyle on windows with spaces in path names Oct 6, 2014 James W. MacDonald depends on packages providing classes Oct 28, 2014

Joseph Nathaniel Paulson

Last active: Oct 25, 2014
1 msg
Joseph Nathaniel Paulson rhdf5 help Oct 25, 2014

Julian Gehring

Last active: Oct 17, 2014
1 msg
Julian Gehring Link posting guide in support forum Oct 17, 2014

Kamal

Last active: Oct 27, 2014
1 msg
Kamal compEpiTools and methylPipe Oct 27, 2014

Kasper Daniel Hansen

Last active: Oct 28, 2014
3 msgs
Kasper Daniel Hansen Updating package NEWS files for Bioconductor 3.0 release announcement Oct 8, 2014 Kasper Daniel Hansen depends on packages providing classes Oct 28, 2014 Kasper Daniel Hansen depends on packages providing classes Oct 28, 2014

Kevin Coombes

Last active: Oct 20, 2014
5 msgs
Kevin Coombes plotPCA for BiocGenerics Oct 20, 2014 Kevin Coombes plotPCA for BiocGenerics Oct 20, 2014 Kevin Coombes plotPCA for BiocGenerics Oct 20, 2014 Kevin Coombes plotPCA for BiocGenerics Oct 20, 2014 Kevin Coombes plotPCA for BiocGenerics Oct 20, 2014

Kevin Rue-Albrecht

Last active: Oct 17, 2014
9 msgs
Kevin Rue-Albrecht GOexpress: new package to visualise microarray and RNAseq data using gene ontology annotations Oct 7, 2014 Kevin Rue-Albrecht no more commits allowed before release ? Oct 10, 2014 Kevin Rue-Albrecht no more commits allowed before release ? Oct 10, 2014 Kevin Rue-Albrecht no more commits allowed before release ? Oct 10, 2014 Kevin Rue-Albrecht no more commits allowed before release ? Oct 10, 2014 Kevin Rue-Albrecht Bioonductor package tracker has moved Oct 16, 2014 Kevin Rue-Albrecht "'BiocInstaller' package not in repository" error during nightly build Oct 16, 2014 Kevin Rue-Albrecht "'BiocInstaller' package not in repository" error during nightly build Oct 16, 2014 Kevin Rue-Albrecht Change of schema of ENSEMBL biomart Oct 17, 2014

Laurent Gatto

Last active: Oct 30, 2014
2 msgs
Laurent Gatto experiment data package versioning Oct 30, 2014 Laurent Gatto experiment data package versioning Oct 30, 2014

Leo Lahti

Last active: Oct 6, 2014
6 msgs
Leo Lahti Rmarkdown built html vignette not included in final package tarball Oct 6, 2014 Leo Lahti Rmarkdown built html vignette not included in final package tarball Oct 6, 2014 Leo Lahti Rmarkdown built html vignette not included in final package tarball Oct 6, 2014 Leo Lahti Rmarkdown built html vignette not included in final package tarball Oct 6, 2014 Leo Lahti Rmarkdown built html vignette not included in final package tarball Oct 6, 2014 Leo Lahti Rmarkdown built html vignette not included in final package tarball Oct 6, 2014

Leonardo Collado Torres

Last active: Oct 31, 2014
15 msgs
Leonardo Collado Torres AnnotationDbi::loadDb() now requires dbType and dbPackage? Oct 10, 2014 Leonardo Collado Torres AnnotationDbi::loadDb() now requires dbType and dbPackage? Oct 10, 2014 Leonardo Collado Torres AnnotationDbi::loadDb() now requires dbType and dbPackage? Oct 10, 2014 Leonardo Collado Torres Git-svn bridge for BioC 3.0 Oct 14, 2014 Leonardo Collado Torres Git-svn bridge for BioC 3.0 Oct 14, 2014 Leonardo Collado Torres runnable examples for internal function ? Oct 16, 2014 Leonardo Collado Torres Why be default 'D' is not dropped from coverage? Oct 18, 2014 Leonardo Collado Torres Why be default 'D' is not dropped from coverage? Oct 21, 2014 Leonardo Collado Torres A more flexible GenomeInfoDb::mapSeqlevels(): used supported info but don't break with new organisms/toy examples Oct 21, 2014 Leonardo Collado Torres Whom to contact for adding an organism to GenomeInfoDb? Oct 21, 2014 Leonardo Collado Torres Whom to contact for adding an organism to GenomeInfoDb? Oct 22, 2014 Leonardo Collado Torres A more flexible GenomeInfoDb::mapSeqlevels(): used supported info but don't break with new organisms/toy examples Oct 22, 2014 Leonardo Collado Torres A more flexible GenomeInfoDb::mapSeqlevels(): used supported info but don't break with new organisms/toy examples Oct 22, 2014 Leonardo Collado Torres A more flexible GenomeInfoDb::mapSeqlevels(): used supported info but don't break with new organisms/toy examples Oct 23, 2014 Leonardo Collado Torres More than 1 citation in landing page Oct 31, 2014

Luo Weijun

Last active: Oct 8, 2014
2 msgs
Luo Weijun Keep the bioc-help email list running? Oct 8, 2014 Luo Weijun Keep the bioc-help email list running? Oct 8, 2014

Marc Carlson

Last active: Oct 16, 2014
2 msgs
Marc Carlson AnnotationDbi::loadDb() now requires dbType and dbPackage? Oct 10, 2014 Marc Carlson How to update annotation packages Oct 16, 2014

Martin Morgan

Last active: Oct 11, 2014
14 msgs
Martin Morgan odd vignette dependency issue Oct 6, 2014 Martin Morgan Bug in GenomicRanges:::compare Oct 6, 2014 Martin Morgan NAMESPACE question Oct 6, 2014 Martin Morgan odd vignette dependency issue Oct 6, 2014 Martin Morgan BiocStyle on windows with spaces in path names Oct 6, 2014 Martin Morgan BiocStyle on windows with spaces in path names Oct 6, 2014 Martin Morgan NAMESPACE question Oct 7, 2014 Martin Morgan NAMESPACE question Oct 7, 2014 Martin Morgan NAMESPACE question Oct 7, 2014 Martin Morgan BiocStyle on windows with spaces in path names Oct 8, 2014 Martin Morgan Keep the bioc-help email list running? Oct 8, 2014 Martin Morgan NAMESPACE question Oct 9, 2014 Martin Morgan AnnotationDbi::loadDb() now requires dbType and dbPackage? Oct 10, 2014 Martin Morgan 'semantically rich' subsetting of SummarizedExperiments Oct 11, 2014

Martin, Tiphaine

Last active: Oct 17, 2014
8 msgs
Martin, Tiphaine Non-ASCII in datase from Biomart EMBL via Gviz package Oct 12, 2014 Martin, Tiphaine Non-ASCII in datase from Biomart EMBL via Gviz package Oct 13, 2014 Martin, Tiphaine runnable examples for internal function ? Oct 13, 2014 Martin, Tiphaine runnable examples for internal function ? Oct 13, 2014 Martin, Tiphaine runnable examples for internal function ? Oct 15, 2014 Martin, Tiphaine error about Display environment/ biomart for the build of my package Oct 16, 2014 Martin, Tiphaine runnable examples for internal function ? Oct 16, 2014 Martin, Tiphaine Change of schema of ENSEMBL biomart Oct 17, 2014

Michael Lawrence

Last active: Oct 31, 2014
19 msgs
Michael Lawrence GenomicFiles: some random issues Oct 3, 2014 Michael Lawrence droplevels method for DataFrame? Oct 6, 2014 Michael Lawrence NAMESPACE question Oct 7, 2014 Michael Lawrence NAMESPACE question Oct 7, 2014 Michael Lawrence S4Vectors unit tests Oct 7, 2014 Michael Lawrence droplevels method for DataFrame? Oct 7, 2014 Michael Lawrence NAMESPACE question Oct 7, 2014 Michael Lawrence 'semantically rich' subsetting of SummarizedExperiments Oct 11, 2014 Michael Lawrence warning when merging disjoint sets of seqlevels Oct 12, 2014 Michael Lawrence warning when merging disjoint sets of seqlevels Oct 13, 2014 Michael Lawrence runnable examples for internal function ? Oct 13, 2014 Michael Lawrence 'semantically rich' subsetting of SummarizedExperiments Oct 13, 2014 Michael Lawrence VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem Oct 24, 2014 Michael Lawrence VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem Oct 24, 2014 Michael Lawrence depends on packages providing classes Oct 28, 2014 Michael Lawrence depends on packages providing classes Oct 28, 2014 Michael Lawrence depends on packages providing classes Oct 29, 2014 Michael Lawrence plotPCA for BiocGenerics Oct 31, 2014 Michael Lawrence plotPCA for BiocGenerics Oct 31, 2014

Michael Love

Last active: Oct 27, 2014
7 msgs
Michael Love GenomicFiles: chunking Oct 1, 2014 Michael Love DESeq2 time series - How to set the experimental design Oct 8, 2014 Michael Love plotPCA for BiocGenerics Oct 20, 2014 Michael Love plotPCA for BiocGenerics Oct 20, 2014 Michael Love plotPCA for BiocGenerics Oct 20, 2014 Michael Love plotPCA for BiocGenerics Oct 20, 2014 Michael Love GenomicFiles: chunking Oct 27, 2014

Michael Turewicz

Last active: Oct 13, 2014
1 msg
Michael Turewicz New package: PAA Oct 13, 2014

Mike

Last active: Oct 22, 2014
1 msg
Mike check warning of QUALIFIER package Oct 22, 2014

Nadia Kamal

Last active: Oct 8, 2014
1 msg
Nadia Kamal DESeq2 time series - How to set the experimental design Oct 8, 2014

Neumann, Steffen

Last active: Oct 6, 2014
1 msg
Neumann, Steffen BiocStyle on windows with spaces in path names Oct 6, 2014

Panagiotis Moulos

Last active: Oct 17, 2014
1 msg
Panagiotis Moulos Change of schema of ENSEMBL biomart Oct 17, 2014

Peter Hickey

Last active: Oct 5, 2014
1 msg
Peter Hickey Bug in GenomicRanges:::compare Oct 5, 2014

Rahmatallah, Yasir

Last active: Oct 27, 2014
1 msg
Rahmatallah, Yasir Announcing the new R pakage GSAR Oct 27, 2014

Ramon Diaz-Uriarte

Last active: Oct 3, 2014
1 msg
Ramon Diaz-Uriarte minor suggestion for BiocStyle? Oct 3, 2014

Robert Castelo

Last active: Oct 24, 2014
11 msgs
Robert Castelo NAMESPACE question Oct 5, 2014 Robert Castelo NAMESPACE question Oct 7, 2014 Robert Castelo NAMESPACE question Oct 7, 2014 Robert Castelo NAMESPACE question Oct 9, 2014 Robert Castelo NAMESPACE question Oct 10, 2014 Robert Castelo How to update annotation packages Oct 15, 2014 Robert Castelo "'BiocInstaller' package not in repository" error during nightly build Oct 16, 2014 Robert Castelo VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem Oct 23, 2014 Robert Castelo VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem Oct 24, 2014 Robert Castelo VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem Oct 24, 2014 Robert Castelo VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem Oct 24, 2014

Robert M. Flight

Last active: Oct 10, 2014
1 msg
Robert M. Flight no more commits allowed before release ? Oct 10, 2014

Rory Stark

Last active: Oct 6, 2014
2 msgs
Rory Stark Error running table() on an RleList returned by coverage() Oct 6, 2014 Rory Stark Error running table() on an RleList returned by coverage() Oct 6, 2014

Ryan

Last active: Oct 31, 2014
3 msgs
Ryan droplevels method for DataFrame? Oct 6, 2014 Ryan droplevels method for DataFrame? Oct 6, 2014 Ryan plotPCA for BiocGenerics Oct 31, 2014

Sean Davis

Last active: Oct 30, 2014
3 msgs
Sean Davis Rmarkdown built html vignette not included in final package tarball Oct 6, 2014 Sean Davis Request for Comments on The NIH Software Discovery Index--a system for linking software, publications and users in the research community Oct 7, 2014 Sean Davis getting a listing of all src packages Oct 30, 2014

Setia Pramana

Last active: Oct 3, 2014
1 msg
Setia Pramana Add a new developer/maintainer Oct 3, 2014

Steve Lianoglou

Last active: Oct 31, 2014
1 msg
Steve Lianoglou plotPCA for BiocGenerics Oct 31, 2014

Thomas Girke

Last active: Oct 9, 2014
1 msg
Thomas Girke Faculty Position in Computational Systems Biology at UC Riverside Oct 9, 2014

Thomas Lin Pedersen

Last active: Oct 31, 2014
3 msgs
Thomas Lin Pedersen plotPCA for BiocGenerics Oct 21, 2014 Thomas Lin Pedersen plotPCA for BiocGenerics Oct 31, 2014 Thomas Lin Pedersen plotPCA for BiocGenerics Oct 31, 2014

Thomas Maurel

Last active: Oct 17, 2014
1 msg
Thomas Maurel Change of schema of ENSEMBL biomart Oct 17, 2014

Tim Triche, Jr.

Last active: Oct 31, 2014
3 msgs
Tim Triche, Jr. Bioonductor package tracker has moved Oct 15, 2014 Tim Triche, Jr. Bioonductor package tracker has moved Oct 15, 2014 Tim Triche, Jr. plotPCA for BiocGenerics Oct 31, 2014

Valerie Obenchain

Last active: Oct 27, 2014
7 msgs
Valerie Obenchain October Newsletter Oct 1, 2014 Valerie Obenchain How to update annotation packages Oct 16, 2014 Valerie Obenchain VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem Oct 23, 2014 Valerie Obenchain VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem Oct 24, 2014 Valerie Obenchain GenomicFiles: chunking Oct 27, 2014 Valerie Obenchain GenomicFiles: chunking Oct 27, 2014 Valerie Obenchain GenomicFiles: chunking Oct 27, 2014

Vincent Carey

Last active: Oct 29, 2014
10 msgs
Vincent Carey a warning we may not need any more? Oct 9, 2014 Vincent Carey 'semantically rich' subsetting of SummarizedExperiments Oct 11, 2014 Vincent Carey 'semantically rich' subsetting of SummarizedExperiments Oct 11, 2014 Vincent Carey Non-ASCII in datase from Biomart EMBL via Gviz package Oct 12, 2014 Vincent Carey Documentation on how to update a BioC experimental package? Oct 23, 2014 Vincent Carey depends on packages providing classes Oct 28, 2014 Vincent Carey depends on packages providing classes Oct 28, 2014 Vincent Carey depends on packages providing classes Oct 28, 2014 Vincent Carey depends on packages providing classes Oct 28, 2014 Vincent Carey depends on packages providing classes Oct 29, 2014

Wolfgang Huber

Last active: Oct 14, 2014
2 msgs
Wolfgang Huber Add a new developer/maintainer Oct 3, 2014 Wolfgang Huber European Bioconductor Developers' Meeting 12th-13th January 2015, Heidelberg Oct 14, 2014

Yinming Jiao

Last active: Oct 9, 2014
1 msg
Yinming Jiao package ‘FEM’ is not available (for R version 3.0.2) Oct 9, 2014

zhao shilin

Last active: Oct 16, 2014
2 msgs
zhao shilin Bioonductor package tracker has moved Oct 15, 2014 zhao shilin Bioonductor package tracker has moved Oct 16, 2014