Bioc-devel - October 2013 - Subject View

BioC 2.13 branch created

1 msg · Oct 14

Dan Tenenbaum BioC 2.13 branch created Oct 14, 2013

Bioconductor 2.13 is released

1 msg · Oct 15

Dan Tenenbaum Bioconductor 2.13 is released Oct 15, 2013

CexoR: new Bioconductor package for peak-pair calling in ChIP-exo data with replicates

1 msg · Oct 13

Pedro Madrigal CexoR: new Bioconductor package for peak-pair calling in ChIP-exo data with replicates Oct 13, 2013

Courtesy message about the upcoming release

1 msg · Oct 4

Marc Carlson Courtesy message about the upcoming release Oct 4, 2013

DNaseR - a new Bioconductor package for DNase-seq digital genomic footprinting

1 msg · Oct 11

Pedro Madrigal DNaseR - a new Bioconductor package for DNase-seq digital genomic footprinting Oct 11, 2013

Emergent build and check errors on the Windows Server Re: release builds have stopped

2 msgs · Oct 9 – Oct 9

Luo Weijun Emergent build and check errors on the Windows Server Re: release builds have stopped Oct 9, 2013 Dan Tenenbaum Emergent build and check errors on the Windows Server Re: release builds have stopped Oct 9, 2013

European Developers' Meeting 2013

1 msg · Oct 30

Jonathan Cairns European Developers' Meeting 2013 Oct 30, 2013

Freezen download statistics for packages

9 msgs · Oct 29 – Oct 31

GenomicRanges, masking problem

2 msgs · Oct 29 – Oct 29

Johannes Waage GenomicRanges, masking problem Oct 29, 2013 Michael Lawrence GenomicRanges, masking problem Oct 29, 2013

Heatplus Heatmap Fails for Hidden Dendrogram and Labels

3 msgs · Oct 13 – Oct 14

Dario Strbenac Heatplus Heatmap Fails for Hidden Dendrogram and Labels Oct 13, 2013 Alexander Ploner Heatplus Heatmap Fails for Hidden Dendrogram and Labels Oct 14, 2013 Dario Strbenac Heatplus Heatmap Fails for Hidden Dendrogram and Labels Oct 14, 2013

IMPORTANT inst/doc/*Rnw to vignettes/

5 msgs · Oct 18 – Oct 21

Martin Morgan IMPORTANT inst/doc/*Rnw to vignettes/ Oct 18, 2013 Gordon K Smyth IMPORTANT inst/doc/*Rnw to vignettes/ Oct 20, 2013 Martin Morgan IMPORTANT inst/doc/*Rnw to vignettes/ Oct 20, 2013 Gordon K Smyth IMPORTANT inst/doc/*Rnw to vignettes/ Oct 20, 2013 Kasper Daniel Hansen IMPORTANT inst/doc/*Rnw to vignettes/ Oct 21, 2013

Important: Bioconductor 2.13 branch to be created today

1 msg · Oct 14

Dan Tenenbaum Important: Bioconductor 2.13 branch to be created today Oct 14, 2013

Is it too late to make an update to an existing package?

1 msg · Oct 7

Dan Tenenbaum Is it too late to make an update to an existing package? Oct 7, 2013

Is it too late to make an update to an existing package?

1 msg · Oct 7

Frederic Fournier Is it too late to make an update to an existing package? Oct 7, 2013

Linking to HTML documents in a package on the BioC web site

3 msgs · Oct 17 – Oct 17

Julian Gehring Linking to HTML documents in a package on the BioC web site Oct 17, 2013 Dan Tenenbaum Linking to HTML documents in a package on the BioC web site Oct 17, 2013 Yihui Xie Linking to HTML documents in a package on the BioC web site Oct 17, 2013

New Bioconductor package: ArrayTV

1 msg · Sep 30

Eitan Halper-Stromberg New Bioconductor package: ArrayTV Sep 30, 2013

New package for meta-analysis in RNA-seq (metaSeq)

1 msg · Oct 24

露崎弘毅 New package for meta-analysis in RNA-seq (metaSeq) Oct 24, 2013

New pvectorize implementation

1 msg · Oct 3

Ryan New pvectorize implementation Oct 3, 2013

Preparing package release notes

1 msg · Oct 8

Dan Tenenbaum Preparing package release notes Oct 8, 2013

Problem with GRanges

5 msgs · Oct 15 – Oct 15

Kristoffer Knudsen Problem with GRanges Oct 15, 2013 Michael Lawrence Problem with GRanges Oct 15, 2013 Martin Morgan Problem with GRanges Oct 15, 2013 Martin Morgan Problem with GRanges Oct 15, 2013 Kristoffer Knudsen Problem with GRanges Oct 15, 2013

Proof-of-concept parallel preloading FastqStreamer

2 msgs · Oct 2 – Oct 2

Gregoire Pau Proof-of-concept parallel preloading FastqStreamer Oct 2, 2013 Martin Morgan Proof-of-concept parallel preloading FastqStreamer Oct 2, 2013

Reminder: Warning deadline approaching

1 msg · Oct 4

Dan Tenenbaum Reminder: Warning deadline approaching Oct 4, 2013

Running Perl Scripts from R package

5 msgs · Oct 23 – Oct 23

Warden, Charles Running Perl Scripts from R package Oct 23, 2013 Gabriel Becker Running Perl Scripts from R package Oct 23, 2013 Dan Tenenbaum Running Perl Scripts from R package Oct 23, 2013 Warden, Charles Running Perl Scripts from R package Oct 23, 2013 Hervé Pagès Running Perl Scripts from R package Oct 23, 2013

SUGGESTION: BioC version (e.g. 2.13) to also follow the x.y(.z) version scheme of Bioc packages

5 msgs · Oct 16 – Oct 17

Henrik Bengtsson SUGGESTION: BioC version (e.g. 2.13) to also follow the x.y(.z) version scheme of Bioc packages Oct 16, 2013 Michael Lawrence SUGGESTION: BioC version (e.g. 2.13) to also follow the x.y(.z) version scheme of Bioc packages Oct 16, 2013 Dan Tenenbaum SUGGESTION: BioC version (e.g. 2.13) to also follow the x.y(.z) version scheme of Bioc packages Oct 16, 2013 Henrik Bengtsson SUGGESTION: BioC version (e.g. 2.13) to also follow the x.y(.z) version scheme of Bioc packages Oct 16, 2013 Nicolas Delhomme SUGGESTION: BioC version (e.g. 2.13) to also follow the x.y(.z) version scheme of Bioc packages Oct 17, 2013

Subsetting an RleList object

14 msgs · Oct 25 – Oct 30

Update policy on experiment data and annotation packages

2 msgs · Oct 10 – Oct 16

Julian Gehring Update policy on experiment data and annotation packages Oct 10, 2013 Marc Carlson Update policy on experiment data and annotation packages Oct 16, 2013

biocValid, update

1 msg · Oct 22

Kasper Daniel Hansen biocValid, update Oct 22, 2013

build server

4 msgs · Oct 5 – Oct 5

Kasper Daniel Hansen build server Oct 5, 2013 Dan Tenenbaum build server Oct 5, 2013 Dan Tenenbaum build server Oct 5, 2013 Kasper Daniel Hansen build server Oct 5, 2013

could bsseq::data.frame2GRanges be added to GenomicRanges

11 msgs · Oct 6 – Oct 8

how could I get new packages list

5 msgs · Oct 11 – Oct 11

Ou, Jianhong how could I get new packages list Oct 11, 2013 Dan Tenenbaum how could I get new packages list Oct 11, 2013 Dan Tenenbaum how could I get new packages list Oct 11, 2013 Ou, Jianhong how could I get new packages list Oct 11, 2013 Dan Tenenbaum how could I get new packages list Oct 11, 2013

isActiveSeq deprecated

2 msgs · Oct 1 – Oct 1

Hahne, Florian isActiveSeq deprecated Oct 1, 2013 Hervé Pagès isActiveSeq deprecated Oct 1, 2013

new package (flipflop)

3 msgs · Oct 22 – Oct 22

Elsa Bernard new package (flipflop) Oct 22, 2013 Julian Gehring new package (flipflop) Oct 22, 2013 Elsa Bernard new package (flipflop) Oct 22, 2013

odd param behavior with scanBam from Rsamtools 1.14.1

3 msgs · Oct 31 – Oct 31

Jason Byars odd param behavior with scanBam from Rsamtools 1.14.1 Oct 31, 2013 Martin Morgan odd param behavior with scanBam from Rsamtools 1.14.1 Oct 31, 2013 Jason Byars odd param behavior with scanBam from Rsamtools 1.14.1 Oct 31, 2013

oneChannelGUI devel

3 msgs · Oct 3 – Oct 3

rcaloger oneChannelGUI devel Oct 3, 2013 rcaloger oneChannelGUI devel Oct 3, 2013 Dan Tenenbaum oneChannelGUI devel Oct 3, 2013

release builds have stopped

1 msg · Oct 9

Dan Tenenbaum release builds have stopped Oct 9, 2013

rtracklayer: problem with formatting the output of ucscTableQuery

7 msgs · Oct 9 – Oct 10

laurent jacob rtracklayer: problem with formatting the output of ucscTableQuery Oct 9, 2013 Michael Lawrence rtracklayer: problem with formatting the output of ucscTableQuery Oct 9, 2013 Kasper Daniel Hansen rtracklayer: problem with formatting the output of ucscTableQuery Oct 9, 2013 Michael Lawrence rtracklayer: problem with formatting the output of ucscTableQuery Oct 9, 2013 Kasper Daniel Hansen rtracklayer: problem with formatting the output of ucscTableQuery Oct 9, 2013 Michael Lawrence rtracklayer: problem with formatting the output of ucscTableQuery Oct 9, 2013 laurent jacob rtracklayer: problem with formatting the output of ucscTableQuery Oct 10, 2013

upgrade instructions at http://bioconductor.org/install/

2 msgs · Oct 24 – Oct 25

Levi Waldron upgrade instructions at http://bioconductor.org/install/ Oct 24, 2013 Martin Morgan upgrade instructions at http://bioconductor.org/install/ Oct 25, 2013

Bioc-devel October 2013

BioC 2.13 branch created

Bioconductor 2.13 is released

CexoR: new Bioconductor package for peak-pair calling in ChIP-exo data with replicates

Courtesy message about the upcoming release

DNaseR - a new Bioconductor package for DNase-seq digital genomic footprinting

Emergent build and check errors on the Windows Server Re: release builds have stopped

European Developers' Meeting 2013

Freezen download statistics for packages

GenomicRanges, masking problem

Heatplus Heatmap Fails for Hidden Dendrogram and Labels

IMPORTANT inst/doc/*Rnw to vignettes/

Important: Bioconductor 2.13 branch to be created today

Is it too late to make an update to an existing package?

Is it too late to make an update to an existing package?

Linking to HTML documents in a package on the BioC web site

New Bioconductor package: ArrayTV

New package for meta-analysis in RNA-seq (metaSeq)

New pvectorize implementation

Preparing package release notes

Problem with GRanges

Proof-of-concept parallel preloading FastqStreamer

Reminder: Warning deadline approaching

Running Perl Scripts from R package

SUGGESTION: BioC version (e.g. 2.13) to also follow the x.y(.z) version scheme of Bioc packages

Subsetting an RleList object

Update policy on experiment data and annotation packages

biocValid, update

build server

could bsseq::data.frame2GRanges be added to GenomicRanges

how could I get new packages list

isActiveSeq deprecated

new package (flipflop)

odd param behavior with scanBam from Rsamtools 1.14.1

oneChannelGUI devel

release builds have stopped

rtracklayer: problem with formatting the output of ucscTableQuery

upgrade instructions at http://bioconductor.org/install/