bioc-sig-sequencing  

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• [Bioc-sig-seq] bioc-sig-sequencing list will be removed Dan Tenenbaum
• [Bioc-sig-seq] Posting to the Bioconductor list without subscribing Dan Tenenbaum
• [Bioc-sig-seq] Another ScanBamParam suggestion Ivan Gregoretti
  • Re: [Bioc-sig-seq] Another ScanBamParam suggestion Martin Morgan
  • Re: [Bioc-sig-seq] Another ScanBamParam suggestion Ivan Gregoretti
• [Bioc-sig-seq] ScanBamParam suggestion Janet Young
  • Re: [Bioc-sig-seq] ScanBamParam suggestion Martin Morgan
• [Bioc-sig-seq] a wired problem wang peter
  • Re: [Bioc-sig-seq] a wired problem Harris A. Jaffee
  • Re: [Bioc-sig-seq] a wired problem Harris A. Jaffee
• [Bioc-sig-seq] coverage vector longer than covered area (ScanBam and IRanges)? Francesco Lescai
• [Bioc-sig-seq] what is wang peter
  • Re: [Bioc-sig-seq] what is Harris A. Jaffee
• [Bioc-sig-seq] Read big fastq files in chunks Anita Lerch
  • Re: [Bioc-sig-seq] Read big fastq files in chunks Martin Morgan
  • Re: [Bioc-sig-seq] Read big fastq files in chunks Anita Lerch
• [Bioc-sig-seq] question about trimLRPatterns wang peter
  • Re: [Bioc-sig-seq] question about trimLRPatterns Harris A. Jaffee
• [Bioc-sig-seq] remove adaptor before remove barcode wang peter
  • Re: [Bioc-sig-seq] remove adaptor before remove barcode Harris A. Jaffee
  • Re: [Bioc-sig-seq] remove adaptor before remove barcode wang peter
  • Re: [Bioc-sig-seq] remove adaptor before remove barcode Harris A. Jaffee
• [Bioc-sig-seq] how to write a fasta file wang peter
  • Re: [Bioc-sig-seq] how to write a fasta file Martin Morgan
• [Bioc-sig-seq] Reads in 3'utr rohan bareja
  • Re: [Bioc-sig-seq] Reads in 3'utr Valerie Obenchain
  • Re: [Bioc-sig-seq] Reads in 3'utr rohan bareja
  • Re: [Bioc-sig-seq] Reads in 3'utr Valerie Obenchain
  • Re: [Bioc-sig-seq] Reads in 3'utr rohan bareja
  • Re: [Bioc-sig-seq] Reads in 3'utr Valerie Obenchain
  • Re: [Bioc-sig-seq] Reads in 3'utr rohan bareja
  • Re: [Bioc-sig-seq] Reads in 3'utr Valerie Obenchain
• [Bioc-sig-seq] first remove low quality or adaptor wang peter
  • Re: [Bioc-sig-seq] first remove low quality or adaptor Hervé Pagès
• [Bioc-sig-seq] how to subset reads or seqs wang peter
  • Re: [Bioc-sig-seq] how to subset reads or seqs wang peter
  • Re: [Bioc-sig-seq] how to subset reads or seqs Hervé Pagès
  • Re: [Bioc-sig-seq] how to subset reads or seqs wang peter
  • Re: [Bioc-sig-seq] how to subset reads or seqs Hervé Pagès
• [Bioc-sig-seq] the question about fastx_clipper wang peter
• [Bioc-sig-seq] how to sort reads by ids wang peter
  • Re: [Bioc-sig-seq] how to sort reads by ids wang peter
  • Re: [Bioc-sig-seq] how to sort reads by ids Martin Morgan
  • Re: [Bioc-sig-seq] how to sort reads by ids wang peter
  • Re: [Bioc-sig-seq] how to sort reads by ids Martin Morgan
• [Bioc-sig-seq] large BAM files and large BED files Rene Paradis
  • Re: [Bioc-sig-seq] large BAM files and large BED files Michael Lawrence
  • Re: [Bioc-sig-seq] large BAM files and large BED files Martin Morgan
  • Re: [Bioc-sig-seq] large BAM files and large BED files Rene Paradis
  • Re: [Bioc-sig-seq] large BAM files and large BED files Martin Morgan
  • Re: [Bioc-sig-seq] large BAM files and large BED files Michael Lawrence
  • Re: [Bioc-sig-seq] large BAM files and large BED files Martin Morgan
  • Re: [Bioc-sig-seq] large BAM files and large BED files Rene Paradis
  • Re: [Bioc-sig-seq] large BAM files and large BED files Martin Morgan
  • Re: [Bioc-sig-seq] large BAM files and large BED files Rene Paradis
  • [Bioc-sig-seq] large BAM files and large bed files Rene Paradis
• [Bioc-sig-seq] edgeR tagwise estimates not converging to common estimate with large prior.n value Sean Ruddy
  • [Bioc-sig-seq] edgeR tagwise estimates not converging to common estimate with large prior.n value Gordon K Smyth
  • Re: [Bioc-sig-seq] edgeR tagwise estimates not converging to common estimate with large prior.n value Sean Ruddy
• [Bioc-sig-seq] a question about write file wang peter
  • Re: [Bioc-sig-seq] a question about write file Vincent Carey
  • Re: [Bioc-sig-seq] a question about write file wang peter
  • Re: [Bioc-sig-seq] a question about write file Martin Morgan
  • Re: [Bioc-sig-seq] a question about write file wang peter
• [Bioc-sig-seq] Course: Introduction to R / Bioconductor for Sequence Analysis, October 17-18 Martin Morgan
  • Re: [Bioc-sig-seq] Course: Introduction to R / Bioconductor for Sequence Analysis, October 17-18 Martin Morgan
• [Bioc-sig-seq] who have tag-clean software wang peter
  • Re: [Bioc-sig-seq] who have tag-clean software Steve Lianoglou
  • Re: [Bioc-sig-seq] who have tag-clean software wang peter
• [Bioc-sig-seq] question about N wang peter
  • Re: [Bioc-sig-seq] question about N Martin Morgan
  • Re: [Bioc-sig-seq] question about N Steve Lianoglou
• [Bioc-sig-seq] About PhredQuality wang peter
  • Re: [Bioc-sig-seq] About PhredQuality Martin Morgan
  • Re: [Bioc-sig-seq] About PhredQuality wang peter
  • Re: [Bioc-sig-seq] About PhredQuality Martin Morgan
• [Bioc-sig-seq] question about replace wang peter
  • Re: [Bioc-sig-seq] question about replace Martin Morgan
• [Bioc-sig-seq] about N statistics wang peter
  • Re: [Bioc-sig-seq] about N statistics Steve Lianoglou
  • Re: [Bioc-sig-seq] about N statistics wang peter
  • Re: [Bioc-sig-seq] about N statistics Martin Morgan
• [Bioc-sig-seq] who have RNA-seq pipeline code wang peter
  • Re: [Bioc-sig-seq] who have RNA-seq pipeline code Martin Morgan
  • Re: [Bioc-sig-seq] who have RNA-seq pipeline code wang peter
  • Re: [Bioc-sig-seq] who have RNA-seq pipeline code Steve Lianoglou
• [Bioc-sig-seq] a question wang peter
  • Re: [Bioc-sig-seq] a question Martin Morgan
  • Re: [Bioc-sig-seq] a question Joseph Scandura
  • Re: [Bioc-sig-seq] a question wang peter
• [Bioc-sig-seq] gaoshan wang peter
  • Re: [Bioc-sig-seq] gaoshan Sean Davis
  • Re: [Bioc-sig-seq] gaoshan wang peter
• [Bioc-sig-seq] using Cuffdiff with biological replicates Jane Merlevede
  • Re: [Bioc-sig-seq] using Cuffdiff with biological replicates Martin Morgan
  • Re: [Bioc-sig-seq] using Cuffdiff with biological replicates Jane Merlevede
• [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Sonia Leach
  • Re: [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Zhu, Lihua (Julie)
  • Re: [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Zhu, Lihua (Julie)
  • Re: [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Ou, Jianhong
  • Re: [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Sonia Leach
  • Re: [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Ou, Jianhong
• [Bioc-sig-seq] edgeR glmLRT contrast Argument Dario Strbenac
  • [Bioc-sig-seq] edgeR glmLRT contrast Argument Gordon K Smyth
• [Bioc-sig-seq] a question about trimLRPatterns wang peter
  • Re: [Bioc-sig-seq] a question about trimLRPatterns Harris A. Jaffee
  • Re: [Bioc-sig-seq] a question about trimLRPatterns Harris A. Jaffee
  • Re: [Bioc-sig-seq] a question about trimLRPatterns wang peter
  • Re: [Bioc-sig-seq] a question about trimLRPatterns Harris A. Jaffee
• [Bioc-sig-seq] import.bw to Rle? [re-opened] Cook, Malcolm
  • Re: [Bioc-sig-seq] import.bw to Rle? [re-opened] Michael Lawrence
• [Bioc-sig-seq] extract non-zero rows Estefania Mancini
  • Re: [Bioc-sig-seq] extract non-zero rows Dario Strbenac
  • Re: [Bioc-sig-seq] extract non-zero rows Davis McCarthy
  • Re: [Bioc-sig-seq] extract non-zero rows Dario Strbenac
  • Re: [Bioc-sig-seq] extract non-zero rows Estefania Mancini
• [Bioc-sig-seq] HPC/Linux Systems Administrator Position Thomas Girke
• [Bioc-sig-seq] edgeR datasets Jérôme Laroche
  • Re: [Bioc-sig-seq] edgeR datasets Guffanti Alessandro
  • Re: [Bioc-sig-seq] edgeR datasets Davis McCarthy
• [Bioc-sig-seq] assess how many duplicated reads Kunbin Qu
  • Re: [Bioc-sig-seq] assess how many duplicated reads Sean Davis
  • Re: [Bioc-sig-seq] assess how many duplicated reads Martin Morgan
  • Re: [Bioc-sig-seq] assess how many duplicated reads Thomas Girke
• [Bioc-sig-seq] edgeR/454 Estefania Mancini
  • Re: [Bioc-sig-seq] edgeR/454 Mark Robinson
  • Re: [Bioc-sig-seq] edgeR/454 Davis McCarthy
• [Bioc-sig-seq] using DEXSeq for up and down regulated exons Jane Merlevede
  • Re: [Bioc-sig-seq] using DEXSeq for up and down regulated exons Wolfgang Huber
  • Re: [Bioc-sig-seq] using DEXSeq for up and down regulated exons Jane Merlevede
  • Re: [Bioc-sig-seq] using DEXSeq for up and down regulated exons Dario Strbenac
• [Bioc-sig-seq] problem when using DEXSeq on genes with 1 exon only Jane Merlevede
  • Re: [Bioc-sig-seq] problem when using DEXSeq on genes with 1 exon only Wolfgang Huber
  • Re: [Bioc-sig-seq] problem when using DEXSeq on genes with 1 exon only Simon Anders
• Re: [Bioc-sig-seq] GRangesList with duplicate names - WORKAROUND Cook, Malcolm
  • Re: [Bioc-sig-seq] GRangesList with duplicate names - WORKAROUND Hervé Pagès
  • Re: [Bioc-sig-seq] GRangesList with duplicate names - WORKAROUND Cook, Malcolm
• [Bioc-sig-seq] DESeq Bogdan Tanasa
  • Re: [Bioc-sig-seq] DESeq Nicolas Delhomme
• [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Ivan Gregoretti
  • Re: [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Hervé Pagès
  • Re: [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Ivan Gregoretti
  • Re: [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Martin Morgan
  • Re: [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Kasper Daniel Hansen
  • Re: [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Hervé Pagès
• [Bioc-sig-seq] differential binding Bogdan Tanasa
  • Re: [Bioc-sig-seq] differential binding Mark Robinson
• [Bioc-sig-seq] count the coverage base by base Kunbin Qu
  • Re: [Bioc-sig-seq] count the coverage base by base Michael Lawrence
  • Re: [Bioc-sig-seq] count the coverage base by base Kunbin Qu
  • Re: [Bioc-sig-seq] count the coverage base by base Michael Lawrence
  • Re: [Bioc-sig-seq] count the coverage base by base Kunbin Qu
  • Re: [Bioc-sig-seq] count the coverage base by base Michael Lawrence
  • Re: [Bioc-sig-seq] count the coverage base by base Kunbin Qu
  • Re: [Bioc-sig-seq] count the coverage base by base Kunbin Qu
  • Re: [Bioc-sig-seq] count the coverage base by base Michael Lawrence
• [Bioc-sig-seq] scanBam memory issue Francesco Lescai
  • Re: [Bioc-sig-seq] scanBam memory issue Steve Lianoglou
  • Re: [Bioc-sig-seq] scanBam memory issue Martin Morgan
• [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Jane Merlevede
  • Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Sean Davis
  • Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Martin Morgan
  • Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Jane Merlevede
  • Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Martin Morgan
  • Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Martin Morgan
  • Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Jane Merlevede
• [Bioc-sig-seq] minoverlap error in countOverlaps Kunbin Qu
  • Re: [Bioc-sig-seq] minoverlap error in countOverlaps Steve Lianoglou
• [Bioc-sig-seq] extract gene symbol error Kunbin Qu
  • Re: [Bioc-sig-seq] extract gene symbol error Steve Lianoglou
• [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Gordon K Smyth
  • Re: [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Sean Ruddy
  • Re: [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Kasper Daniel Hansen
  • Re: [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Sean Ruddy
  • Re: [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Gordon K Smyth
  • Re: [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Gordon K Smyth
• [Bioc-sig-seq] psetdiff on GRangesLists Error Dario Strbenac
  • Re: [Bioc-sig-seq] psetdiff on GRangesLists Error Hervé Pagès
• [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Sean Ruddy
• [Bioc-sig-seq] reduce in ShortRead Kunbin Qu
  • Re: [Bioc-sig-seq] reduce in ShortRead Kasper Daniel Hansen
• [Bioc-sig-seq] Supplying own variance functions and adjusted counts to a DESeq dataset Gordon K Smyth
  • Re: [Bioc-sig-seq] Supplying own variance functions and adjusted counts to a DESeq dataset Sean Ruddy
  • [Bioc-sig-seq] "pooled" dispersion estimation in edgeR Gordon K Smyth
  • Re: [Bioc-sig-seq] "pooled" dispersion estimation in edgeR Sean Ruddy
  • Re: [Bioc-sig-seq] "pooled" dispersion estimation in edgeR Gordon K Smyth
  • Re: [Bioc-sig-seq] "pooled" dispersion estimation in edgeR Sean Ruddy
• [Bioc-sig-seq] scanBam segfault Ivan Gregoretti
  • Re: [Bioc-sig-seq] scanBam segfault Martin Morgan
  • Re: [Bioc-sig-seq] scanBam segfault Martin Morgan
  • Re: [Bioc-sig-seq] scanBam segfault Ivan Gregoretti
• [Bioc-sig-seq] Supplying own variance functions and adjusted counts to a DESeq dataset Sean Ruddy
  • Re: [Bioc-sig-seq] Supplying own variance functions and adjusted counts to a DESeq dataset Simon Anders
  • Re: [Bioc-sig-seq] Supplying own variance functions and adjusted counts to a DESeq dataset Simon Anders
• [Bioc-sig-seq] using GenomicFeatures Jason Lu
  • Re: [Bioc-sig-seq] using GenomicFeatures Michael Lawrence
• [Bioc-sig-seq] Loading large BAM files Ivan Gregoretti
  • Re: [Bioc-sig-seq] Loading large BAM files Kasper Daniel Hansen
  • Re: [Bioc-sig-seq] Loading large BAM files Ivan Gregoretti
  • Re: [Bioc-sig-seq] Loading large BAM files Martin Morgan

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