bioc-sig-sequencing  

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• • Re: [Bioc-sig-seq] seqselect on SimpleRleList and RangesList - bug? and request Michael Lawrence
• [Bioc-sig-seq] Browser display question [email protected]
  • Re: [Bioc-sig-seq] Browser display question Michael Lawrence
• [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Steve Lianoglou
  • Re: [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Michael Lawrence
  • Re: [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Stuart Andrews
  • Re: [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Vincent Carey
  • Re: [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Vincent Carey
  • Re: [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Stuart Andrews
  • Re: [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Steve Lianoglou
  • Re: [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Patrick Aboyoun
  • Re: [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Michael Lawrence
  • Re: [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Charles C. Berry
  • Re: [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Patrick Aboyoun
  • Re: [Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata? Steve Lianoglou
• [Bioc-sig-seq] Two Bioconductor Job Opportunities in Seattle Martin Morgan
• [Bioc-sig-seq] annotatePeakInBatch feature request Dario Strbenac
  • Re: [Bioc-sig-seq] annotatePeakInBatch feature request Zhu, Julie
  • Re: [Bioc-sig-seq] annotatePeakInBatch feature request Dario Strbenac
  • Re: [Bioc-sig-seq] annotatePeakInBatch feature request Dario Strbenac
• [Bioc-sig-seq] Problem installing latest version (1.0.2) RSamtools from Bioconductor kanika arora
  • Re: [Bioc-sig-seq] Problem installing latest version (1.0.2) RSamtools from Bioconductor Martin Morgan
  • Re: [Bioc-sig-seq] Problem installing latest version (1.0.2) RSamtools from Bioconductor Marcus Davy
  • Re: [Bioc-sig-seq] Problem installing latest version (1.0.2) RSamtools from Bioconductor Marcus Davy
  • Re: [Bioc-sig-seq] Problem installing latest version (1.0.2) RSamtools from Bioconductor Martin Morgan
  • Re: [Bioc-sig-seq] Problem installing latest version (1.0.2) RSamtools from Bioconductor Marcus Davy
  • Re: [Bioc-sig-seq] Problem installing latest version (1.0.2) RSamtools from Bioconductor kanika arora
  • Re: [Bioc-sig-seq] Problem installing latest version (1.0.2) RSamtools from Bioconductor Martin Morgan
• [Bioc-sig-seq] readBamGappedAlignments() cigar error Craig Johnson
  • Re: [Bioc-sig-seq] readBamGappedAlignments() cigar error Hervé Pagès
• [Bioc-sig-seq] RangedData Ordering Dario Strbenac
  • Re: [Bioc-sig-seq] RangedData Ordering Michael Lawrence
• [Bioc-sig-seq] size of DNAString object Hans-Ulrich Klein
  • Re: [Bioc-sig-seq] size of DNAString object Vincent Carey
  • Re: [Bioc-sig-seq] size of DNAString object Hans-Ulrich Klein
• [Bioc-sig-seq] using subseq() on a DNAStringSet Andrew Yee
  • Re: [Bioc-sig-seq] using subseq() on a DNAStringSet Steve Lianoglou
  • Re: [Bioc-sig-seq] using subseq() on a DNAStringSet Steve Lianoglou
  • Re: [Bioc-sig-seq] using subseq() on a DNAStringSet Andrew Yee
• [Bioc-sig-seq] REVISED BioC 2010 Scholarship Application due date Martin Morgan
• Re: [Bioc-sig-seq] MapProfileShort data error? Gottardo Raphaël
• [Bioc-sig-seq] RangedData::findOverlaps feature request Zhu, Julie
• [Bioc-sig-seq] Could anyone suggest a good software for nucleosome positioning using ChIP-seq data? Xuekui Zhang
  • Re: [Bioc-sig-seq] Could anyone suggest a good software for nucleosome positioning using ChIP-seq data? Martin Morgan
• [Bioc-sig-seq] BioC 2010 Afternoon Practical Proposals Martin Morgan
• [Bioc-sig-seq] News about PICS/rGADEM/MotIV Droit Arnaud
• [Bioc-sig-seq] microarray to RNA-Seq Gordon K Smyth
• [Bioc-sig-seq] quantile normalization for RNA-seq Kunbin Qu
• [Bioc-sig-seq] microarray to RNA-Seq Alper Yilmaz
  • Re: [Bioc-sig-seq] microarray to RNA-Seq Alper Yilmaz
  • Re: [Bioc-sig-seq] microarray to RNA-Seq Wolfgang Huber
• [Bioc-sig-seq] use pipes to map reads with bowtie and convert to BAM joseph
  • Re: [Bioc-sig-seq] use pipes to map reads with bowtie and convert to BAM James W. MacDonald
• [Bioc-sig-seq] ShortRead readAligned Strange Sequences Dario Strbenac
  • Re: [Bioc-sig-seq] ShortRead readAligned Strange Sequences Steve Lianoglou
  • Re: [Bioc-sig-seq] ShortRead readAligned Strange Sequences Dario Strbenac
• [Bioc-sig-seq] determining start position for QualityAlignedXStringSet output from pairwiseAlignment() Andrew Yee
  • Re: [Bioc-sig-seq] determining start position for QualityAlignedXStringSet output from pairwiseAlignment() Patrick Aboyoun
  • Re: [Bioc-sig-seq] determining start position for QualityAlignedXStringSet output from pairwiseAlignment() Andrew Yee
• [Bioc-sig-seq] Calculating RPKMs from Tophat results : Your advice requested Pratap, Abhishek
  • Re: [Bioc-sig-seq] Calculating RPKMs from Tophat results : Your advice requested Steve Lianoglou
• Re: [Bioc-sig-seq] [BioC] ShortRead with BAM Duke
  • Re: [Bioc-sig-seq] [BioC] ShortRead with BAM James W. MacDonald
  • Re: [Bioc-sig-seq] [BioC] ShortRead with BAM Duke
• [Bioc-sig-seq] rdapply(): Going from RangedData to RangedData (not to list) Ivan Gregoretti
  • Re: [Bioc-sig-seq] rdapply(): Going from RangedData to RangedData (not to list) Michael Lawrence
  • Re: [Bioc-sig-seq] rdapply(): Going from RangedData to RangedData (not to list) Ivan Gregoretti
• [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Ivan Gregoretti
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Patrick Aboyoun
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Ivan Gregoretti
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Patrick Aboyoun
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Ivan Gregoretti
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Patrick Aboyoun
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Ivan Gregoretti
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Sean Davis
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Ivan Gregoretti
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Sean Davis
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Patrick Aboyoun
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Chris Seidel
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Martin Morgan
  • [Bioc-sig-seq] IRange overlap percentage Kunbin Qu
  • Re: [Bioc-sig-seq] IRange overlap percentage Michael Lawrence
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Michael Lawrence
  • Re: [Bioc-sig-seq] GRanges, failure assigning chromosome lengths Michael Lawrence
• [Bioc-sig-seq] coverage() is misbehaving with (apparently sound) GRanges object Ivan Gregoretti
  • Re: [Bioc-sig-seq] coverage() is misbehaving with (apparently sound) GRanges object Patrick Aboyoun
  • Re: [Bioc-sig-seq] coverage() is misbehaving with (apparently sound) GRanges object Ivan Gregoretti
• [Bioc-sig-seq] GRanges, RangedData coercion Ivan Gregoretti
  • Re: [Bioc-sig-seq] GRanges, RangedData coercion Michael Lawrence
• [Bioc-sig-seq] Dealing with pileups/duplicates in RNAseq Steve Lianoglou
  • Re: [Bioc-sig-seq] Dealing with pileups/duplicates in RNAseq Sean Davis
• [Bioc-sig-seq] Rsamtools readPileup with Mosaik alignments James MacDonald
  • Re: [Bioc-sig-seq] Rsamtools readPileup with Mosaik alignments James W. MacDonald
  • Re: [Bioc-sig-seq] Rsamtools readPileup with Mosaik alignments Steve Lianoglou
  • Re: [Bioc-sig-seq] Rsamtools readPileup with Mosaik alignments Martin Morgan
• [Bioc-sig-seq] ChIP-seq, peak shape Ivan Gregoretti
• [Bioc-sig-seq] Rsamtools countBam labeling Matthew Young
  • Re: [Bioc-sig-seq] Rsamtools countBam labeling Vincent Carey
  • Re: [Bioc-sig-seq] Rsamtools countBam labeling Matthew Young
• [Bioc-sig-seq] Coverage for RangeList? Jane Landolin
  • Re: [Bioc-sig-seq] Coverage for RangeList? Paul Leo
  • Re: [Bioc-sig-seq] Coverage for RangeList? Patrick Aboyoun
  • Re: [Bioc-sig-seq] Coverage for RangeList? Michael Lawrence
  • Re: [Bioc-sig-seq] Coverage for RangeList? Jane Landolin
• [Bioc-sig-seq] Genominator: strategy for combining multiple AlignedRead objects joseph franklin
  • Re: [Bioc-sig-seq] Genominator: strategy for combining multiple AlignedRead objects Kasper Daniel Hansen
  • Re: [Bioc-sig-seq] Genominator: strategy for combining multiple AlignedRead objects joseph franklin
  • Re: [Bioc-sig-seq] Genominator: strategy for combining multiple AlignedRead objects joseph franklin
  • Re: [Bioc-sig-seq] Genominator: strategy for combining multiple AlignedRead objects Kasper Daniel Hansen
  • Re: [Bioc-sig-seq] Genominator: strategy for combining multiple AlignedRead objects Kasper Daniel Hansen
  • Re: [Bioc-sig-seq] Genominator: strategy for combining multiple AlignedRead objects joseph franklin
• [Bioc-sig-seq] Use rtracklayer to create specific format bed file [email protected]
  • Re: [Bioc-sig-seq] Use rtracklayer to create specific format bed file Michael Lawrence
• [Bioc-sig-seq] write.XStringSet() terribly slow Steffen Neumann
  • Re: [Bioc-sig-seq] write.XStringSet() terribly slow Kasper Daniel Hansen
  • Re: [Bioc-sig-seq] write.XStringSet() terribly slow Kasper Daniel Hansen
  • Re: [Bioc-sig-seq] write.XStringSet() terribly slow Steffen Neumann
  • Re: [Bioc-sig-seq] write.XStringSet() terribly slow Hans-Ulrich Klein
  • Re: [Bioc-sig-seq] write.XStringSet() terribly slow Hervé Pagès
  • Re: [Bioc-sig-seq] write.XStringSet() terribly slow Martin Morgan
  • Re: [Bioc-sig-seq] write.XStringSet() terribly slow Martin Morgan
  • Re: [Bioc-sig-seq] write.XStringSet() terribly slow Hans-Ulrich Klein
• [Bioc-sig-seq] For ChIPpeakAnno Users- [BioC] query and subject hits in findOverlaps through different space names Zhu, Julie
• [Bioc-sig-seq] coordinates 0-indexed or 1-indexed in IRanges? margherita mutarelli
  • Re: [Bioc-sig-seq] coordinates 0-indexed or 1-indexed in IRanges? Michael Lawrence
  • Re: [Bioc-sig-seq] coordinates 0-indexed or 1-indexed in IRanges? Hans-Rudolf Hotz
  • [Bioc-sig-seq] coordinates 0-indexed or 1-indexed in IRanges? margherita mutarelli
  • Re: [Bioc-sig-seq] coordinates 0-indexed or 1-indexed in IRanges? Hans-Rudolf Hotz
  • Re: [Bioc-sig-seq] coordinates 0-indexed or 1-indexed in IRanges? Michael Lawrence
• [Bioc-sig-seq] subsetting a ShortReadQ object joseph
  • Re: [Bioc-sig-seq] subsetting a ShortReadQ object Martin Morgan
• [Bioc-sig-seq] perTile QA element in the FastqQA class Sirisha Sunkara
  • Re: [Bioc-sig-seq] perTile QA element in the FastqQA class Martin Morgan
  • Re: [Bioc-sig-seq] perTile QA element in the FastqQA class Sirisha Sunkara
  • Re: [Bioc-sig-seq] perTile QA element in the FastqQA class Sirisha Sunkara
  • Re: [Bioc-sig-seq] perTile QA element in the FastqQA class Martin Morgan
• [Bioc-sig-seq] Rsamtools scanBam output to Bam burak kutlu
  • Re: [Bioc-sig-seq] Rsamtools scanBam output to Bam Martin Morgan
  • Re: [Bioc-sig-seq] Rsamtools scanBam output to Bam Sean Davis
  • Re: [Bioc-sig-seq] Rsamtools scanBam output to Bam burak kutlu
• [Bioc-sig-seq] putting Paired-End Illumina reads together Lana Schaffer
• [Bioc-sig-seq] mget with case-insensitive keys xuxiang086
  • Re: [Bioc-sig-seq] mget with case-insensitive keys Martin Morgan
  • Re: [Bioc-sig-seq] mget with case-insensitive keys xuxiang086
  • Re: [Bioc-sig-seq] mget with case-insensitive keys Laurent Gautier
• [Bioc-sig-seq] GenomicFeatures vignette, question on findOverlaps results? [email protected]
  • Re: [Bioc-sig-seq] GenomicFeatures vignette, question on findOverlaps results? Patrick Aboyoun
• [Bioc-sig-seq] read counts of multiple samples across all regions Kunbin Qu
  • Re: [Bioc-sig-seq] read counts of multiple samples across all regions Vincent Carey
• [Bioc-sig-seq] Rsamtools append burak kutlu
  • Re: [Bioc-sig-seq] Rsamtools append Martin Morgan
• [Bioc-sig-seq] GenomicFeatures vignette, problem findOverlaps and 'seqnames' naming convention? [email protected]
  • Re: [Bioc-sig-seq] GenomicFeatures vignette, problem findOverlaps and 'seqnames' naming convention? Vincent Carey
• [Bioc-sig-seq] using value in RangedData Kunbin Qu
  • Re: [Bioc-sig-seq] using value in RangedData Michael Lawrence
  • Re: [Bioc-sig-seq] using value in RangedData Charles C. Berry
  • [Bioc-sig-seq] counts differences among multiple RNA-seq samples Kunbin Qu
  • [Bioc-sig-seq] counts differences among multiple RNA-seq samples Kunbin Qu
  • Re: [Bioc-sig-seq] counts differences among multiple RNA-seq samples Nicolas Delhomme
  • Re: [Bioc-sig-seq] counts differences among multiple RNA-seq samples Kasper Daniel Hansen
  • Re: [Bioc-sig-seq] counts differences among multiple RNA-seq samples Nicolas Delhomme
  • Re: [Bioc-sig-seq] counts differences among multiple RNA-seq samples Kunbin Qu
• [Bioc-sig-seq] GenomicFeatures, error in type conversion RangeData to GRanges [email protected]
  • Re: [Bioc-sig-seq] GenomicFeatures, error in type conversion RangeData to GRanges Martin Morgan
  • Re: [Bioc-sig-seq] GenomicFeatures, error in type conversion RangeData to GRanges Michael Lawrence
  • Re: [Bioc-sig-seq] GenomicFeatures, error in type conversion RangeData to GRanges Martin Morgan
  • Re: [Bioc-sig-seq] GenomicFeatures, error in type conversion RangeData to GRanges Michael Lawrence
  • Re: [Bioc-sig-seq] GenomicFeatures, error in type conversion RangeData to GRanges Michael Lawrence
  • Re: [Bioc-sig-seq] GenomicFeatures, error in type conversion RangeData to GRanges Patrick Aboyoun
  • Re: [Bioc-sig-seq] GenomicFeatures, error in type conversion RangeData to GRanges Michael Lawrence
  • Re: [Bioc-sig-seq] GenomicFeatures, error in type conversion RangeData to GRanges Patrick Aboyoun
  • Re: [Bioc-sig-seq] GenomicFeatures, error in type conversion RangeData to GRanges Michael Lawrence
• [Bioc-sig-seq] ExpressionSet alikes for next-gen data David Rossell
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data Michael Lawrence
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data David Rossell
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data Michael Lawrence
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data David Rossell
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data Martin Morgan
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data Vincent Carey
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data Michael Lawrence
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data Vincent Carey
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data Michael Lawrence
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data Vincent Carey
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data Martin Morgan
  • Re: [Bioc-sig-seq] ExpressionSet alikes for next-gen data Vincent Carey
• [Bioc-sig-seq] ChIP-seq analysis in normalization/peak calling between sample and control Chen-Yi Chen
  • Re: [Bioc-sig-seq] ChIP-seq analysis in normalization/peak calling between sample and control Muino, Jose
  • Re: [Bioc-sig-seq] ChIP-seq analysis in normalization/peak calling between sample and control Chen-Yi Chen
  • Re: [Bioc-sig-seq] ChIP-seq analysis in normalization/peak calling between sample and control Muino, Jose
  • Re: [Bioc-sig-seq] ChIP-seq analysis in normalization/peak calling between sample and control Raphael Gottardo
• [Bioc-sig-seq] On re-installing R/Bioconductor. Ivan Gregoretti
  • Re: [Bioc-sig-seq] On re-installing R/Bioconductor. Patrick Aboyoun
  • Re: [Bioc-sig-seq] On re-installing R/Bioconductor. Michael Lawrence
  • Re: [Bioc-sig-seq] On re-installing R/Bioconductor. Ivan Gregoretti
• [Bioc-sig-seq] Fastq File size limit in the Short Read Package Sirisha Sunkara
  • Re: [Bioc-sig-seq] Fastq File size limit in the Short Read Package Martin Morgan
  • Re: [Bioc-sig-seq] Fastq File size limit in the Short Read Package Martin Morgan
• [Bioc-sig-seq] Questions about coverage visualization in wig file output Chen-Yi (Charlie) Chen
  • [Bioc-sig-seq] Questions about coverage visualization in wig file output Chen-Yi Chen
  • Re: [Bioc-sig-seq] Questions about coverage visualization in wig file output Michael Lawrence

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