bioc-sig-sequencing  

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• • Re: [Bioc-sig-seq] readAligned and BAM format Sean Davis
  • Re: [Bioc-sig-seq] readAligned and BAM format Pratap, Abhishek
  • Re: [Bioc-sig-seq] readAligned and BAM format Sean Davis
  • Re: [Bioc-sig-seq] readAligned and BAM format Laurent Gautier
  • Re: [Bioc-sig-seq] readAligned and BAM format Martin Morgan
• [Bioc-sig-seq] ChIP-seq normalization Bogdan Tanasa
• [Bioc-sig-seq] filter fastQ based on quality score? Jennifer Wernegreen
  • Re: [Bioc-sig-seq] filter fastQ based on quality score? Martin Morgan
• [Bioc-sig-seq] GenomicFeatures package [email protected]
  • Re: [Bioc-sig-seq] GenomicFeatures package Michael Lawrence
  • Re: [Bioc-sig-seq] GenomicFeatures package Martin Morgan
  • Re: [Bioc-sig-seq] GenomicFeatures package Steve Lianoglou
  • Re: [Bioc-sig-seq] GenomicFeatures package Martin Morgan
  • Re: [Bioc-sig-seq] GenomicFeatures package Michael Lawrence
  • Re: [Bioc-sig-seq] GenomicFeatures package Seth Falcon
  • Re: [Bioc-sig-seq] GenomicFeatures package Steve Lianoglou
  • Re: [Bioc-sig-seq] GenomicFeatures package Seth Falcon
  • Re: [Bioc-sig-seq] GenomicFeatures package Steve Lianoglou
• [Bioc-sig-seq] Paired end reads -tools? Paul Leo
  • Re: [Bioc-sig-seq] Paired end reads -tools? Nicolas Delhomme
• [Bioc-sig-seq] coverage ranges included in gene ranges and input data Florence Cavalli
  • Re: [Bioc-sig-seq] coverage ranges included in gene ranges and input data Michael Lawrence
  • Re: [Bioc-sig-seq] coverage ranges included in gene ranges and input data Patrick Aboyoun
  • Re: [Bioc-sig-seq] coverage ranges included in gene ranges and input data Florence Cavalli
• [Bioc-sig-seq] Error message when working with IRanges package [email protected]
  • Re: [Bioc-sig-seq] Error message when working with IRanges package Michael Lawrence
  • Re: [Bioc-sig-seq] Error message when working with IRanges package Michael Lawrence
• Re: [Bioc-sig-seq] gdapply, coverage, and widths for all chromosomes Chris Seidel
• [Bioc-sig-seq] gdapply, coverage, and widths for all chromosomes Chris Seidel
  • Re: [Bioc-sig-seq] gdapply, coverage, and widths for all chromosomes Deepayan Sarkar
  • Re: [Bioc-sig-seq] gdapply, coverage, and widths for all chromosomes Michael Lawrence
  • Re: [Bioc-sig-seq] gdapply, coverage, and widths for all chromosomes Martin Morgan
  • Re: [Bioc-sig-seq] gdapply, coverage, and widths for all chromosomes Michael Lawrence
• [Bioc-sig-seq] rtracklayer and coverage() from GenomeData Chris Seidel
  • Re: [Bioc-sig-seq] rtracklayer and coverage() from GenomeData Michael Lawrence
• [Bioc-sig-seq] coverage to wig joseph
  • Re: [Bioc-sig-seq] coverage to wig Michael Lawrence
• [Bioc-sig-seq] Mean coverage of capture regions Dykema, Karl
  • Re: [Bioc-sig-seq] Mean coverage of capture regions Sean Davis
  • Re: [Bioc-sig-seq] Mean coverage of capture regions Patrick Aboyoun
• [Bioc-sig-seq] trimLRPatterns question joseph
  • Re: [Bioc-sig-seq] trimLRPatterns question Harris A. Jaffee
• [Bioc-sig-seq] Fwd: SFC#00118080 - Control over file name format? Michael Muratet
  • Re: [Bioc-sig-seq] Fwd: SFC#00118080 - Control over file name format? Martin Morgan
• [Bioc-sig-seq] Getting file names from list.files in a more useful order Michael Muratet
  • Re: [Bioc-sig-seq] Getting file names from list.files in a more useful order Martin Morgan
  • Re: [Bioc-sig-seq] Getting file names from list.files in a more useful order Michael Muratet
• [Bioc-sig-seq] New Bioconductor team member Martin Morgan
• [Bioc-sig-seq] Trouble loading development version of ShortRead on OS X Michael Muratet
  • Re: [Bioc-sig-seq] Trouble loading development version of ShortRead on OS X Martin Morgan
  • Re: [Bioc-sig-seq] Trouble loading development version of ShortRead on OS X Michael Muratet
  • Re: [Bioc-sig-seq] Trouble loading development version of ShortRead on OS X Michael Muratet
• [Bioc-sig-seq] ShortRead and Solexa GA(II) Matthew McCormack
  • Re: [Bioc-sig-seq] ShortRead and Solexa GA(II) Martin Morgan
• [Bioc-sig-seq] WIG from coverage Seidel, Christopher
  • Re: [Bioc-sig-seq] WIG from coverage Michael Lawrence
  • Re: [Bioc-sig-seq] WIG from coverage Michael Lawrence
  • Re: [Bioc-sig-seq] WIG from coverage Ivan Gregoretti
  • Re: [Bioc-sig-seq] WIG from coverage Chris Seidel
  • Re: [Bioc-sig-seq] WIG from coverage Michael Lawrence
  • Re: [Bioc-sig-seq] WIG from coverage Michael Lawrence
  • Re: [Bioc-sig-seq] WIG from coverage Michael Lawrence
• [Bioc-sig-seq] ChIP-seq readReads question [email protected]
  • Re: [Bioc-sig-seq] ChIP-seq readReads question Patrick Aboyoun
• [Bioc-sig-seq] Update only specific spaces of RangedData Christian Ruckert
  • Re: [Bioc-sig-seq] Update only specific spaces of RangedData Patrick Aboyoun
  • Re: [Bioc-sig-seq] Update only specific spaces of RangedData Michael Lawrence
  • Re: [Bioc-sig-seq] Update only specific spaces of RangedData Patrick Aboyoun
  • Re: [Bioc-sig-seq] Update only specific spaces of RangedData Michael Lawrence
  • Re: [Bioc-sig-seq] Update only specific spaces of RangedData Patrick Aboyoun
• [Bioc-sig-seq] Minimal short sequences position/orientation container Ivan Gregoretti
  • Re: [Bioc-sig-seq] Minimal short sequences position/orientation container Patrick Aboyoun
  • Re: [Bioc-sig-seq] Minimal short sequences position/orientation container Ivan Gregoretti
  • Re: [Bioc-sig-seq] Minimal short sequences position/orientation container Sean Davis
  • Re: [Bioc-sig-seq] Minimal short sequences position/orientation container Ivan Gregoretti
• [Bioc-sig-seq] BED to WIG format conversion Ivan Gregoretti
  • Re: [Bioc-sig-seq] BED to WIG format conversion Michael Lawrence
  • Re: [Bioc-sig-seq] BED to WIG format conversion Sean Davis
  • Re: [Bioc-sig-seq] BED to WIG format conversion Ivan Gregoretti
  • Re: [Bioc-sig-seq] BED to WIG format conversion Michael Lawrence
  • Re: [Bioc-sig-seq] BED to WIG format conversion Patrick Aboyoun
  • Re: [Bioc-sig-seq] BED to WIG format conversion Michael Lawrence
  • Re: [Bioc-sig-seq] BED to WIG format conversion Patrick Aboyoun
  • Re: [Bioc-sig-seq] BED to WIG format conversion Michael Lawrence
  • Re: [Bioc-sig-seq] BED to WIG format conversion Patrick Aboyoun
  • Re: [Bioc-sig-seq] BED to WIG format conversion Michael Lawrence
  • Re: [Bioc-sig-seq] BED to WIG format conversion Ivan Gregoretti
  • Re: [Bioc-sig-seq] BED to WIG format conversion Michael Lawrence
  • Re: [Bioc-sig-seq] BED to WIG format conversion Sean Davis
• [Bioc-sig-seq] Annotation of the lactococcus lactis genome Karin Bjerre
  • Re: [Bioc-sig-seq] Annotation of the lactococcus lactis genome Marc Carlson
  • Re: [Bioc-sig-seq] Annotation of the lactococcus lactis genome Marc Carlson
• [Bioc-sig-seq] Rolexa quality scores Fuad Gwadry
• [Bioc-sig-seq] Creating TSS Regions IRanges with Strand Information Dario Strbenac
  • Re: [Bioc-sig-seq] Creating TSS Regions IRanges with Strand Information Michael Lawrence
  • Re: [Bioc-sig-seq] Creating TSS Regions IRanges with Strand Information Dario Strbenac
  • Re: [Bioc-sig-seq] Creating TSS Regions IRanges with Strand Information Michael Lawrence
• [Bioc-sig-seq] Question when running ShortRead to generate a QA report [email protected]
  • Re: [Bioc-sig-seq] Question when running ShortRead to generate a QA report Martin Morgan
• [Bioc-sig-seq] IRanges::overlap interface, help writing idiomatic code? Steve Lianoglou
  • Re: [Bioc-sig-seq] IRanges::overlap interface, help writing idiomatic code? Michael Lawrence
  • Re: [Bioc-sig-seq] IRanges::overlap interface, help writing idiomatic code? Steve Lianoglou
  • Re: [Bioc-sig-seq] IRanges::overlap interface, help writing idiomatic code? Patrick Aboyoun
  • Re: [Bioc-sig-seq] IRanges::overlap interface, help writing idiomatic code? Michael Lawrence
  • Re: [Bioc-sig-seq] IRanges::overlap interface, help writing idiomatic code? Patrick Aboyoun
  • Re: [Bioc-sig-seq] IRanges::overlap interface, help writing idiomatic code? Martin Morgan
  • Re: [Bioc-sig-seq] IRanges::overlap interface, help writing idiomatic code? Steve Lianoglou
  • Re: [Bioc-sig-seq] IRanges::overlap interface, help writing idiomatic code? Patrick Aboyoun
  • Re: [Bioc-sig-seq] IRanges::overlap interface, help writing idiomatic code? Steve Lianoglou
• [Bioc-sig-seq] Slow/hanged QA on Illumina Data Pratap, Abhishek
  • Re: [Bioc-sig-seq] Slow/hanged QA on Illumina Data Ivan Gregoretti
  • Re: [Bioc-sig-seq] Slow/hanged QA on Illumina Data Pratap, Abhishek
  • Re: [Bioc-sig-seq] Slow/hanged QA on Illumina Data Martin Morgan
  • Re: [Bioc-sig-seq] Slow/hanged QA on Illumina Data Harris A. Jaffee
• [Bioc-sig-seq] Running rtracklayer vignette [email protected]
  • Re: [Bioc-sig-seq] Running rtracklayer vignette Michael Lawrence
• [Bioc-sig-seq] Problems with diffPeakSummary Sini Junttila
• Re: [Bioc-sig-seq] release of chipseq package xiaoa
  • Re: [Bioc-sig-seq] release of chipseq package Patrick Aboyoun
• [Bioc-sig-seq] AlignedRead and complex subsetting Ivan Gregoretti
  • Re: [Bioc-sig-seq] AlignedRead and complex subsetting Steve Lianoglou
  • Re: [Bioc-sig-seq] AlignedRead and complex subsetting Martin Morgan
  • Re: [Bioc-sig-seq] AlignedRead and complex subsetting Ivan Gregoretti
  • Re: [Bioc-sig-seq] AlignedRead and complex subsetting Patrick Aboyoun
  • Re: [Bioc-sig-seq] AlignedRead and complex subsetting Martin Morgan
  • Re: [Bioc-sig-seq] AlignedRead and complex subsetting Ivan Gregoretti
  • Re: [Bioc-sig-seq] AlignedRead and complex subsetting Martin Morgan
  • Re: [Bioc-sig-seq] AlignedRead and complex subsetting Michael Lawrence
  • Re: [Bioc-sig-seq] AlignedRead and complex subsetting Martin Morgan
• [Bioc-sig-seq] Consolidate AlignedRead objects Ivan Gregoretti
  • Re: [Bioc-sig-seq] Consolidate AlignedRead objects Martin Morgan
  • Re: [Bioc-sig-seq] Consolidate AlignedRead objects Ivan Gregoretti
  • Re: [Bioc-sig-seq] Consolidate AlignedRead objects Martin Morgan
• Re: [Bioc-sig-seq] frequency of A, C, G, T Nenad Bartonicek
  • Re: [Bioc-sig-seq] frequency of A, C, G, T Ali Mohamadian
  • Re: [Bioc-sig-seq] frequency of A, C, G, T Patrick Aboyoun
• [Bioc-sig-seq] ShortRead: puzzled with memory issues over readAligned, readFasta and qa Leonardo Collado Torres
  • Re: [Bioc-sig-seq] ShortRead: puzzled with memory issues over readAligned, readFasta and qa Martin Morgan
  • [Bioc-sig-seq] Illumina CIF format for ShortRead? Michael Muratet
  • Re: [Bioc-sig-seq] Illumina CIF format for ShortRead? Martin Morgan
  • Re: [Bioc-sig-seq] Illumina CIF format for ShortRead? Martin Morgan
  • Re: [Bioc-sig-seq] Illumina CIF format for ShortRead? Michael Muratet
• [Bioc-sig-seq] tag density plots Bogdan Tanasa
  • Re: [Bioc-sig-seq] tag density plots Michael Lawrence
  • Re: [Bioc-sig-seq] tag density plots Bogdan Tanasa
• [Bioc-sig-seq] 2D plots Bogdan Tanasa
  • Re: [Bioc-sig-seq] 2D plots Michael Lawrence
  • Re: [Bioc-sig-seq] 2D plots Bogdan Tanasa
  • Re: [Bioc-sig-seq] 2D plots gbucci
• [Bioc-sig-seq] readAligned and coverage methods of the short read package Sirisha Sunkara
  • Re: [Bioc-sig-seq] readAligned and coverage methods of the short read package Martin Morgan
  • Re: [Bioc-sig-seq] readAligned and coverage methods of the short read package Sirisha Sunkara
  • Re: [Bioc-sig-seq] readAligned and coverage methods of the short read package Martin Morgan
  • [Bioc-sig-seq] frequency of A, C, G, T Ali Mohamadian
• [Bioc-sig-seq] using shortRead for Bowtie alignments burak kutlu
  • Re: [Bioc-sig-seq] using shortRead for Bowtie alignments James Bullard
  • Re: [Bioc-sig-seq] using shortRead for Bowtie alignments Martin Morgan
  • Re: [Bioc-sig-seq] using shortRead for Bowtie alignments burak kutlu
• Re: [Bioc-sig-seq] Rle, RleViews Simon Anders
  • Re: [Bioc-sig-seq] Rle, RleViews Michael Lawrence
  • Re: [Bioc-sig-seq] Rle, RleViews Patrick Aboyoun
• [Bioc-sig-seq] Import Solexa Data John Lande
  • Re: [Bioc-sig-seq] Import Solexa Data Martin Morgan
• [Bioc-sig-seq] Assessing Transcriptome Coverage Abhishek Pratap
  • Re: [Bioc-sig-seq] Assessing Transcriptome Coverage Abhishek Pratap
  • Re: [Bioc-sig-seq] Assessing Transcriptome Coverage Sean Davis
  • Re: [Bioc-sig-seq] Assessing Transcriptome Coverage Abhishek Pratap
  • Re: [Bioc-sig-seq] Assessing Transcriptome Coverage Sean Davis
  • Re: [Bioc-sig-seq] Assessing Transcriptome Coverage Abhishek Pratap
  • Re: [Bioc-sig-seq] Assessing Transcriptome Coverage Michael Dondrup
• [Bioc-sig-seq] What to do when single reads make up a large percentage of counts? Jenny Drnevich
  • Re: [Bioc-sig-seq] What to do when single reads make up a large percentage of counts? Ludo Pagie
• [Bioc-sig-seq] AlignedRead and IRanges James Bullard
  • Re: [Bioc-sig-seq] AlignedRead and IRanges Martin Morgan
  • [Bioc-sig-seq] Peaks Ali Mohamadian
  • Re: [Bioc-sig-seq] Peaks Deepayan Sarkar
• [Bioc-sig-seq] match, vmatch James Bullard
  • Re: [Bioc-sig-seq] match, vmatch Hervé Pagès
• [Bioc-sig-seq] Problem with ShortRead reading quality scores from bowtie Fuad Gwadry
  • Re: [Bioc-sig-seq] Problem with ShortRead reading quality scores from bowtie Martin Morgan
  • Re: [Bioc-sig-seq] Problem with ShortRead reading quality scores from bowtie Martin Morgan
  • Re: [Bioc-sig-seq] Problem with ShortRead reading quality scores from bowtie Fuad Gwadry
  • Re: [Bioc-sig-seq] Problem with ShortRead reading quality scores from bowtie Martin Morgan
  • Re: [Bioc-sig-seq] Problem with ShortRead reading quality scores from bowtie Fuad Gwadry
  • Re: [Bioc-sig-seq] Problem with ShortRead reading quality scores from bowtie Martin Morgan
  • [Bioc-sig-seq] alignQuality Fuad Gwadry
  • Re: [Bioc-sig-seq] alignQuality Martin Morgan
  • Re: [Bioc-sig-seq] Reading quality scores from Bowtie (using Piple Fuad Gwadry
  • Re: [Bioc-sig-seq] Reading quality scores from Bowtie (using Piple Martin Morgan
  • Re: [Bioc-sig-seq] Problem with ShortRead reading quality scores from bowtie Martin Morgan
• [Bioc-sig-seq] readAligned in ShortRead package Ingunn Berget
  • Re: [Bioc-sig-seq] readAligned in ShortRead package Martin Morgan
  • Re: [Bioc-sig-seq] readAligned in ShortRead package Martin Morgan
  • Re: [Bioc-sig-seq] readAligned in ShortRead package Ingunn Berget
• [Bioc-sig-seq] How to graphical represent different views on a reference genomic sequence Purnachander
  • Re: [Bioc-sig-seq] How to graphical represent different views on a reference genomic sequence Patrick Aboyoun
  • Re: [Bioc-sig-seq] How to graphical represent different views on a reference genomic sequence Michael Lawrence
• [Bioc-sig-seq] fastq2fasta joseph
  • Re: [Bioc-sig-seq] fastq2fasta Martin Morgan
  • Re: [Bioc-sig-seq] fastq2fasta joseph

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