Bioc-devel - February 2013 - Thread View

[Bioc-devel] VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry

8 msgs Feb 28

Julian Gehring VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry Feb 26, 2013

Richard Pearson VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry Feb 26, 2013

Julian Gehring VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry Feb 26, 2013

Sean Davis VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry Feb 26, 2013

Valerie Obenchain VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry Feb 26, 2013

Valerie Obenchain VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry Feb 27, 2013

Julian Gehring VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry Feb 28, 2013

Valerie Obenchain VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry Feb 28, 2013

[Bioc-devel] ensemblVEP: 'fork' argument for 'VEPParam' should be integer

2 msgs Feb 27

Julian Gehring ensemblVEP: 'fork' argument for 'VEPParam' should be integer Feb 27, 2013

Valerie Obenchain ensemblVEP: 'fork' argument for 'VEPParam' should be integer Feb 27, 2013

[Bioc-devel] I would like to publish a bioconductor package.

4 msgs Feb 27

Davide Rambaldi I would like to publish a bioconductor package. Feb 27, 2013

Stephanie M. Gogarten I would like to publish a bioconductor package. Feb 27, 2013

Hervé Pagès I would like to publish a bioconductor package. Feb 27, 2013

[Bioc-devel] build error on RIPSeeker

1 msg Feb 26

Dan Tenenbaum build error on RIPSeeker Feb 26, 2013

[Bioc-devel] build error on RIPSeeker

1 msg Feb 26

Yue Li build error on RIPSeeker Feb 26, 2013

[Bioc-devel] changed 'split' behavior

1 msg Feb 26

Martin Morgan changed 'split' behavior Feb 26, 2013

[Bioc-devel] why doesn't this ``just work'' ? (defined coercion is ignored by S3 method?)

3 msgs Feb 26

Tim Triche, Jr. why doesn't this ``just work'' ? (defined coercion is ignored by S3 method?) Feb 26, 2013

Hervé Pagès why doesn't this ``just work'' ? (defined coercion is ignored by S3 method?) Feb 26, 2013

Tim Triche, Jr. why doesn't this ``just work'' ? (defined coercion is ignored by S3 method?) Feb 26, 2013

[Bioc-devel] [VariantAnnotation] segfault thrown when scan header for VCF files out of GATK pipeline

5 msgs Feb 26

Tengfei Yin segfault thrown when scan header for VCF files out of GATK pipeline Feb 19, 2013

Martin Morgan segfault thrown when scan header for VCF files out of GATK pipeline Feb 19, 2013

Tengfei Yin segfault thrown when scan header for VCF files out of GATK pipeline Feb 19, 2013

Tengfei Yin segfault thrown when scan header for VCF files out of GATK pipeline Feb 26, 2013

Martin Morgan segfault thrown when scan header for VCF files out of GATK pipeline Feb 26, 2013

[Bioc-devel] Bioconductor 2.12 release schedule

1 msg Feb 25

Dan Tenenbaum Bioconductor 2.12 release schedule Feb 25, 2013

[Bioc-devel] GRanges construction fails if metadata column is named 'c'

2 msgs Feb 24

Julian Gehring GRanges construction fails if metadata column is named 'c' Feb 22, 2013

Hervé Pagès GRanges construction fails if metadata column is named 'c' Feb 24, 2013

[Bioc-devel] is there such a thing as too much dependency?

2 msgs Feb 22

Stephanie M. Gogarten is there such a thing as too much dependency? Feb 22, 2013

Michael Lawrence is there such a thing as too much dependency? Feb 22, 2013

[Bioc-devel] Webpage spring cleaning - Package submission

3 msgs Feb 22

Wolfgang Huber Webpage spring cleaning - Package submission Feb 22, 2013

Martin Morgan Webpage spring cleaning - Package submission Feb 22, 2013

Tim Triche, Jr. Webpage spring cleaning - Package submission Feb 22, 2013

[Bioc-devel] Request to add 'normalize' to BiocGenerics

17 msgs Feb 21

Laurent Gatto Request to add 'normalize' to BiocGenerics Feb 15, 2013

Hervé Pagès Request to add 'normalize' to BiocGenerics Feb 19, 2013

Diego Diez Request to add 'normalize' to BiocGenerics Feb 19, 2013

Laurent Gatto Request to add 'normalize' to BiocGenerics Feb 20, 2013

Wolfgang Huber Request to add 'normalize' to BiocGenerics Feb 20, 2013

Schalkwyk, Leonard Request to add 'normalize' to BiocGenerics Feb 20, 2013

Laurent Gautier Request to add 'normalize' to BiocGenerics Feb 20, 2013

Hervé Pagès Request to add 'normalize' to BiocGenerics Feb 20, 2013

Wolfgang Huber Request to add 'normalize' to BiocGenerics Feb 20, 2013

cstrato Request to add 'normalize' to BiocGenerics Feb 20, 2013

Robert Gentleman Request to add 'normalize' to BiocGenerics Feb 20, 2013

Hervé Pagès Request to add 'normalize' to BiocGenerics Feb 20, 2013

Laurent Gautier Request to add 'normalize' to BiocGenerics Feb 20, 2013

Hervé Pagès Request to add 'normalize' to BiocGenerics Feb 21, 2013

Wolfgang Huber Request to add 'normalize' to BiocGenerics Feb 21, 2013

Hervé Pagès Request to add 'normalize' to BiocGenerics Feb 21, 2013

[Bioc-devel] Biostrings: XStringViews subsetting operator does not reduce element metadata

2 msgs Feb 21

Jiří Hon Biostrings: XStringViews subsetting operator does not reduce element metadata Feb 21, 2013

Hervé Pagès Biostrings: XStringViews subsetting operator does not reduce element metadata Feb 21, 2013

[Bioc-devel] Section~\ref{sec:bla} idiom in vignettes

3 msgs Feb 21

Wolfgang Huber Section~\ref{sec:bla} idiom in vignettes Feb 3, 2013

Martin Morgan Section~\ref{sec:bla} idiom in vignettes Feb 3, 2013

Dan Tenenbaum Section~\ref{sec:bla} idiom in vignettes Feb 21, 2013

[Bioc-devel] small request on graph::graphBAM()

5 msgs Feb 19

Robert Castelo small request on graph::graphBAM() Feb 6, 2013

Valerie Obenchain small request on graph::graphBAM() Feb 7, 2013

Robert Castelo small request on graph::graphBAM() Feb 7, 2013

Valerie Obenchain small request on graph::graphBAM() Feb 19, 2013

Robert Castelo small request on graph::graphBAM() Feb 19, 2013

[Bioc-devel] (missing?) UCSCKG -> SYMBOL mappings in Homo.sapiens (etc.)

3 msgs Feb 14

Marc Carlson (missing?) UCSCKG -> SYMBOL mappings in Homo.sapiens (etc.) Feb 12, 2013

Marc Carlson (missing?) UCSCKG -> SYMBOL mappings in Homo.sapiens (etc.) Feb 13, 2013

Tim Triche, Jr. (missing?) UCSCKG -> SYMBOL mappings in Homo.sapiens (etc.) Feb 14, 2013

[Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914)

1 msg Feb 14

Cook, Malcolm SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914) Feb 14, 2013

[Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914)

1 msg Feb 14

Cook, Malcolm SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914) Feb 14, 2013

[Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq'

2 msgs Feb 13

Cook, Malcolm SRAdb listSRAfile returns empty datatable with filetype='fastq' Feb 13, 2013

[Bioc-devel] R CMD build not copying PDF vignettes to inst\doc

5 msgs Feb 12

Dan Tenenbaum R CMD build not copying PDF vignettes to inst\doc Feb 7, 2013

Norman Pavelka R CMD build not copying PDF vignettes to inst\doc Feb 12, 2013

Dan Tenenbaum R CMD build not copying PDF vignettes to inst\doc Feb 12, 2013

[Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

8 msgs Feb 12

Tengfei Yin no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file Feb 6, 2013

Marc Carlson no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file Feb 8, 2013

Cook, Malcolm no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file Feb 8, 2013

Marc Carlson no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file Feb 9, 2013

Cook, Malcolm no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file Feb 9, 2013

Tengfei Yin no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file Feb 11, 2013

Marc Carlson no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file Feb 11, 2013

Tengfei Yin no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file Feb 12, 2013

[Bioc-devel] ShortRead: optional custom labeling of samples in QA report

3 msgs Feb 12

Julian Gehring ShortRead: optional custom labeling of samples in QA report Feb 12, 2013

Martin Morgan ShortRead: optional custom labeling of samples in QA report Feb 12, 2013

[Bioc-devel] makeTranscriptDBFromGFF v. Flybase GFF

2 msgs Feb 11

Cook, Malcolm makeTranscriptDBFromGFF v. Flybase GFF Feb 11, 2013

Marc Carlson makeTranscriptDBFromGFF v. Flybase GFF Feb 11, 2013

[Bioc-devel] bug tracker (was Fwd: Reminder: Your Atlassian OnDemand account bioc-internal will be deactivated soon)

2 msgs Feb 9

Dan Tenenbaum bug tracker (was Fwd: Reminder: Your Atlassian OnDemand account bioc-internal will be deactivated soon) Feb 9, 2013

[Bioc-devel] R CMD build not copying PDF vignettes to inst\doc

1 msg Feb 7

Norman Pavelka R CMD build not copying PDF vignettes to inst\doc Feb 7, 2013

[Bioc-devel] oligonucleotideFrequency Performance Enhancement

3 msgs Feb 7

Dario Strbenac oligonucleotideFrequency Performance Enhancement Feb 5, 2013

Hervé Pagès oligonucleotideFrequency Performance Enhancement Feb 7, 2013

Kasper Daniel Hansen oligonucleotideFrequency Performance Enhancement Feb 7, 2013

[Bioc-devel] BioC question

2 msgs Feb 6

Dan Tenenbaum BioC question Feb 6, 2013

Thomas Sandmann BioC question Feb 6, 2013

[Bioc-devel] BioC question

1 msg Feb 6

Thomas Sandmann BioC question Feb 6, 2013

[Bioc-devel] New packages: PathNet and PathNetData

1 msg Feb 5

Jason Smith [Contractor] New packages: PathNet and PathNetData Feb 5, 2013

[Bioc-devel] New package HTSFilter

1 msg Feb 5

Andrea Rau New package HTSFilter Feb 5, 2013

[Bioc-devel] New package casper

1 msg Feb 4

David Rossell New package casper Feb 4, 2013

[Bioc-devel] information about sequencing experiment

4 msgs Feb 3

Michael Love information about sequencing experiment Feb 3, 2013

Martin Morgan information about sequencing experiment Feb 3, 2013

Tim Triche, Jr. information about sequencing experiment Feb 3, 2013

Michael Love information about sequencing experiment Feb 3, 2013

Bioc-devel February 2013