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Bioc-devel December 2013

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Monday, December 30, 2013 2 emails
Markus Riester GSVA and LumiBatch objects Julian Gehring request: high-level seqlevel utilities
Friday, December 27, 2013 6 emails
Michael Lawrence request: high-level seqlevel utilities Valerie Obenchain request: high-level seqlevel utilities Tim Triche, Jr. request: high-level seqlevel utilities Arora, Sonali request: high-level seqlevel utilities Michael Lawrence request: high-level seqlevel utilities Arora, Sonali request: high-level seqlevel utilities
Wednesday, December 25, 2013 1 email
Michael Lawrence request: high-level seqlevel utilities
Tuesday, December 24, 2013 3 emails
Arora, Sonali request: high-level seqlevel utilities Michael Love BigWigViews Valerie Obenchain BigWigViews
Saturday, December 21, 2013 1 email
Hervé Pagès Consistency between miRNATarget and MiRaGE
Friday, December 20, 2013 12 emails
Stephanie M. Gogarten Job opening: Research Scientist in Biostatistics (Seattle, WA) Ou, Jianhong how to use footnote in BiocStyle Ou, Jianhong very slow to use intronsByTranscript in GenomicFeatures Hervé Pagès readGAlignmentPairs function broken? Hervé Pagès very slow to use intronsByTranscript in GenomicFeatures Robert Castelo very slow to use intronsByTranscript in GenomicFeatures Ou, Jianhong very slow to use intronsByTranscript in GenomicFeatures Hervé Pagès very slow to use intronsByTranscript in GenomicFeatures James W. MacDonald very slow to use intronsByTranscript in GenomicFeatures Ou, Jianhong very slow to use intronsByTranscript in GenomicFeatures Ou, Jianhong simple question about floor Hervé Pagès alphabetFrequency on AAString
Thursday, December 19, 2013 16 emails
Luo Weijun Bulky installation and loading triggered by function import Steven McKinney simple question about floor Martin Morgan how to use footnote in BiocStyle Martin Morgan Bulky installation and loading triggered by function import Ou, Jianhong simple question about floor Ou, Jianhong how to use footnote in BiocStyle Leonard Goldstein readGAlignmentPairs function broken? Hervé Pagès readGAlignmentPairs function broken? Kasper Daniel Hansen codetoolsBioC does not suggest methods from packages not defining generic Hervé Pagès readGAlignmentPairs function broken? Leonard Goldstein readGAlignmentPairs function broken? Luo Weijun Bulky installation and loading triggered by function import Michael Lawrence codetoolsBioC does not suggest methods from packages not defining generic Martin Morgan codetoolsBioC does not suggest methods from packages not defining generic Michael Lawrence codetoolsBioC does not suggest methods from packages not defining generic Michael Lawrence codetoolsBioC does not suggest methods from packages not defining generic
Wednesday, December 18, 2013 1 email
Leonard Goldstein readGAlignmentPairs function broken?
Tuesday, December 17, 2013 2 emails
Dan Tenenbaum sequencing workflow Michael Lawrence sequencing workflow
Monday, December 16, 2013 17 emails
Hervé Pagès ordering GenomicRanges without regard for strand Martin Morgan edgeR crashes when xlsxjars is loaded Ryan edgeR crashes when xlsxjars is loaded Ryan edgeR crashes when xlsxjars is loaded Ryan edgeR crashes when xlsxjars is loaded Steve Lianoglou edgeR crashes when xlsxjars is loaded Ryan edgeR crashes when xlsxjars is loaded Martin Morgan edgeR crashes when xlsxjars is loaded Martin Morgan New Seattle Bioconductor group members Dan Tenenbaum edgeR crashes when xlsxjars is loaded Michael Lawrence request: high-level seqlevel utilities Steve Lianoglou edgeR crashes when xlsxjars is loaded Ryan edgeR crashes when xlsxjars is loaded Arora, Sonali request: high-level seqlevel utilities Michael Lawrence request: high-level seqlevel utilities Julian Gehring request: high-level seqlevel utilities Michael Lawrence request: high-level seqlevel utilities
Friday, December 13, 2013 10 emails
Hervé Pagès equivalent of seqselect,vector,Rle Michael Lawrence equivalent of seqselect,vector,Rle Hervé Pagès equivalent of seqselect,vector,Rle Michael Lawrence equivalent of seqselect,vector,Rle Hervé Pagès equivalent of seqselect,vector,Rle Michael Lawrence equivalent of seqselect,vector,Rle Ou, Jianhong error when install ŒRsamtools¹, ŒGenomicAlignments¹ and Œrtracklayer¹ Hervé Pagès error when install ŒRsamtools¹, ŒGenomicAlignments¹ and Œrtracklayer¹ Ou, Jianhong error when install ŒRsamtools¹, ŒGenomicAlignments¹ and Œrtracklayer¹ Hervé Pagès Consistency between miRNATarget and MiRaGE
Thursday, December 12, 2013 7 emails
Kasper Daniel Hansen ordering GenomicRanges without regard for strand Hervé Pagès ordering GenomicRanges without regard for strand Tim Triche, Jr. ordering GenomicRanges without regard for strand Michael Lawrence ordering GenomicRanges without regard for strand Michael Lawrence request: high-level seqlevel utilities Julian Gehring VariantAnnotation: Convertion from VCF to VRanges for CG example VCF Valerie Obenchain VariantAnnotation: Convertion from VCF to VRanges for CG example VCF
Wednesday, December 11, 2013 4 emails
Hervé Pagès forgeBSgenomeDataPkg and gzipped files Nicolas Delhomme Conflict between BiocStyle and the verbatim package Hahne, Florian forgeBSgenomeDataPkg and gzipped files Martin Morgan Conflict between BiocStyle and the verbatim package
Tuesday, December 10, 2013 1 email
Y-h. Taguchi Consistency between miRNATarget and MiRaGE
Monday, December 9, 2013 12 emails
Dan Tenenbaum Errors in recent updates of MiRaGE development release Y-h. Taguchi Errors in recent updates of MiRaGE development release Taku Tokuyasu Rsamtools BAM > SAM? Stephanie M. Gogarten asVCF error coming from normalizeSingleBracketSubscript Hervé Pagès new GenomicAlignments package Valerie Obenchain VariantAnnotation: Convertion from VCF to VRanges for CG example VCF Hervé Pagès XVector: abstraction Kasper Daniel Hansen XVector: abstraction Michael Lawrence XVector: abstraction Laurent Gautier XVector: abstraction Hervé Pagès XVector: abstraction Michael Lawrence XVector: abstraction
Sunday, December 8, 2013 1 email
Hervé Pagès XVector: abstraction
Saturday, December 7, 2013 1 email
Julian Gehring VariantAnnotation: Convertion from VCF to VRanges for CG example VCF
Thursday, December 5, 2013 13 emails
Valerie Obenchain readGAlignmentsList and read groups Michael Lawrence readGAlignmentsList and read groups Valerie Obenchain Rsamtools BAM > SAM? Martin Morgan Rsamtools BAM > SAM? Dan Tenenbaum Package archives Michael Lawrence XVector: abstraction Kasper Daniel Hansen Package archives Michael Lawrence XVector: block-wise compressed rda Kasper Daniel Hansen GenomicRanges: Storing 'seqlengths' as numeric Michael Lawrence Rsamtools BAM > SAM? Nicolas Delhomme GenomicRanges: Storing 'seqlengths' as numeric jens timmerman Package archives Martin Morgan Rsamtools BAM > SAM?
Wednesday, December 4, 2013 5 emails
Dan Tenenbaum How to update a release package? James W. MacDonald How to update a release package? Setia Pramana How to update a release package? Dan Tenenbaum Struggles with correct import ..... Martin Maechler Struggles with correct import .....
Tuesday, December 3, 2013 10 emails
Kasper Daniel Hansen Struggles with correct import ..... Martin Morgan Conflict between BiocStyle and the verbatim package Hervé Pagès GenomicRanges: Storing 'seqlengths' as numeric Nicolas Delhomme Conflict between BiocStyle and the verbatim package Kasper Daniel Hansen GenomicRanges: Storing 'seqlengths' as numeric Hervé Pagès GenomicRanges: Storing 'seqlengths' as numeric Martin Morgan GenomicRanges: Storing 'seqlengths' as numeric Dan Tenenbaum Struggles with correct import ..... Martin Maechler Struggles with correct import ..... Julian Gehring GenomicRanges: Storing 'seqlengths' as numeric
Monday, December 2, 2013 8 emails
Dario Strbenac IlluminaID2nuID Incorrectly Uses If Statement Michael Lawrence feature request: pmax for columns of DataFrame objects Valerie Obenchain [Bioc-devel] [VariantAnnotation] Robert Castelo feature request: pmax for columns of DataFrame objects Valerie Obenchain VariantAnnotation writeVcf problem Michael Lawrence feature request: pmax for columns of DataFrame objects Robert Castelo feature request: pmax for columns of DataFrame objects Gang Feng IlluminaID2nuID Incorrectly Uses If Statement
Sunday, December 1, 2013 1 email
Dario Strbenac IlluminaID2nuID Incorrectly Uses If Statement