bioc-sig-sequencing  

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• 2011/09/30 [Bioc-sig-seq] bioc-sig-sequencing list will be removed Dan Tenenbaum
• 2011/09/30 [Bioc-sig-seq] Posting to the Bioconductor list without subscribing Dan Tenenbaum
• 2011/09/30 Re: [Bioc-sig-seq] Another ScanBamParam suggestion Ivan Gregoretti
• 2011/09/30 Re: [Bioc-sig-seq] Another ScanBamParam suggestion Martin Morgan
• 2011/09/30 [Bioc-sig-seq] Another ScanBamParam suggestion Ivan Gregoretti
• 2011/09/29 Re: [Bioc-sig-seq] ScanBamParam suggestion Martin Morgan
• 2011/09/29 [Bioc-sig-seq] ScanBamParam suggestion Janet Young
• 2011/09/29 Re: [Bioc-sig-seq] as.data.frame on GRanges object with DNAStringSet in values Michael Lawrence
• 2011/09/29 Re: [Bioc-sig-seq] Reads in 3'utr rohan bareja
• 2011/09/28 Re: [Bioc-sig-seq] Reads in 3'utr Valerie Obenchain
• 2011/09/28 Re: [Bioc-sig-seq] a wired problem Harris A. Jaffee
• 2011/09/28 Re: [Bioc-sig-seq] a wired problem Harris A. Jaffee
• 2011/09/28 [Bioc-sig-seq] a wired problem wang peter
• 2011/09/28 [Bioc-sig-seq] coverage vector longer than covered area (ScanBam and IRanges)? Francesco Lescai
• 2011/09/27 Re: [Bioc-sig-seq] question about trimLRPatterns Harris A. Jaffee
• 2011/09/27 Re: [Bioc-sig-seq] what is Harris A. Jaffee
• 2011/09/27 [Bioc-sig-seq] what is wang peter
• 2011/09/27 Re: [Bioc-sig-seq] Reads in 3'utr rohan bareja
• 2011/09/27 Re: [Bioc-sig-seq] remove adaptor before remove barcode Harris A. Jaffee
• 2011/09/27 Re: [Bioc-sig-seq] Read big fastq files in chunks Anita Lerch
• 2011/09/27 Re: [Bioc-sig-seq] Read big fastq files in chunks Martin Morgan
• 2011/09/27 [Bioc-sig-seq] Read big fastq files in chunks Anita Lerch
• 2011/09/26 Re: [Bioc-sig-seq] Reads in 3'utr Valerie Obenchain
• 2011/09/26 Re: [Bioc-sig-seq] remove adaptor before remove barcode wang peter
• 2011/09/26 Re: [Bioc-sig-seq] remove adaptor before remove barcode Harris A. Jaffee
• 2011/09/26 Re: [Bioc-sig-seq] how to subset reads or seqs Hervé Pagès
• 2011/09/26 [Bioc-sig-seq] question about trimLRPatterns wang peter
• 2011/09/26 [Bioc-sig-seq] remove adaptor before remove barcode wang peter
• 2011/09/25 Re: [Bioc-sig-seq] how to write a fasta file Martin Morgan
• 2011/09/25 [Bioc-sig-seq] how to write a fasta file wang peter
• 2011/09/23 Re: [Bioc-sig-seq] Reads in 3'utr Valerie Obenchain
• 2011/09/23 Re: [Bioc-sig-seq] Reads in 3'utr rohan bareja
• 2011/09/23 Re: [Bioc-sig-seq] Reads in 3'utr Valerie Obenchain
• 2011/09/22 [Bioc-sig-seq] Reads in 3'utr rohan bareja
• 2011/09/22 Re: [Bioc-sig-seq] how to subset reads or seqs wang peter
• 2011/09/22 Re: [Bioc-sig-seq] first remove low quality or adaptor Hervé Pagès
• 2011/09/22 Re: [Bioc-sig-seq] how to subset reads or seqs Hervé Pagès
• 2011/09/21 Re: [Bioc-sig-seq] large BAM files and large BED files Rene Paradis
• 2011/09/20 [Bioc-sig-seq] first remove low quality or adaptor wang peter
• 2011/09/20 Re: [Bioc-sig-seq] large BAM files and large BED files Martin Morgan
• 2011/09/20 Re: [Bioc-sig-seq] large BAM files and large BED files Rene Paradis
• 2011/09/19 Re: [Bioc-sig-seq] large BAM files and large BED files Martin Morgan
• 2011/09/19 Re: [Bioc-sig-seq] large BAM files and large BED files Michael Lawrence
• 2011/09/19 Re: [Bioc-sig-seq] how to subset reads or seqs wang peter
• 2011/09/19 [Bioc-sig-seq] how to subset reads or seqs wang peter
• 2011/09/19 Re: [Bioc-sig-seq] large BAM files and large BED files Martin Morgan
• 2011/09/19 Re: [Bioc-sig-seq] large BAM files and large BED files Rene Paradis
• 2011/09/19 [Bioc-sig-seq] the question about fastx_clipper wang peter
• 2011/09/19 [Bioc-sig-seq] large BAM files and large bed files Rene Paradis
• 2011/09/18 Re: [Bioc-sig-seq] how to sort reads by ids Martin Morgan
• 2011/09/18 Re: [Bioc-sig-seq] how to sort reads by ids wang peter
• 2011/09/18 Re: [Bioc-sig-seq] how to sort reads by ids Martin Morgan
• 2011/09/18 Re: [Bioc-sig-seq] how to sort reads by ids wang peter
• 2011/09/18 [Bioc-sig-seq] how to sort reads by ids wang peter
• 2011/09/16 Re: [Bioc-sig-seq] edgeR tagwise estimates not converging to common estimate with large prior.n value Sean Ruddy
• 2011/09/16 [Bioc-sig-seq] edgeR tagwise estimates not converging to common estimate with large prior.n value Gordon K Smyth
• 2011/09/16 Re: [Bioc-sig-seq] large BAM files and large BED files Martin Morgan
• 2011/09/16 Re: [Bioc-sig-seq] large BAM files and large BED files Michael Lawrence
• 2011/09/16 [Bioc-sig-seq] large BAM files and large BED files Rene Paradis
• 2011/09/15 [Bioc-sig-seq] edgeR tagwise estimates not converging to common estimate with large prior.n value Sean Ruddy
• 2011/09/14 Re: [Bioc-sig-seq] a question about write file wang peter
• 2011/09/13 Re: [Bioc-sig-seq] a question about write file Martin Morgan
• 2011/09/13 Re: [Bioc-sig-seq] a question about write file wang peter
• 2011/09/13 Re: [Bioc-sig-seq] a question about write file Vincent Carey
• 2011/09/13 Re: [Bioc-sig-seq] who have tag-clean software wang peter
• 2011/09/13 [Bioc-sig-seq] a question about write file wang peter
• 2011/09/13 Re: [Bioc-sig-seq] Course: Introduction to R / Bioconductor for Sequence Analysis, October 17-18 Martin Morgan
• 2011/09/13 [Bioc-sig-seq] Course: Introduction to R / Bioconductor for Sequence Analysis, October 17-18 Martin Morgan
• 2011/09/12 Re: [Bioc-sig-seq] who have tag-clean software Steve Lianoglou
• 2011/09/12 [Bioc-sig-seq] who have tag-clean software wang peter
• 2011/09/11 Re: [Bioc-sig-seq] About PhredQuality Martin Morgan
• 2011/09/08 Re: [Bioc-sig-seq] About PhredQuality wang peter
• 2011/09/08 Re: [Bioc-sig-seq] question about N Steve Lianoglou
• 2011/09/07 Re: [Bioc-sig-seq] question about N Martin Morgan
• 2011/09/07 Re: [Bioc-sig-seq] question about replace Martin Morgan
• 2011/09/07 [Bioc-sig-seq] question about N wang peter
• 2011/09/07 Re: [Bioc-sig-seq] About PhredQuality Martin Morgan
• 2011/09/07 [Bioc-sig-seq] About PhredQuality wang peter
• 2011/09/07 [Bioc-sig-seq] question about replace wang peter
• 2011/09/06 Re: [Bioc-sig-seq] about N statistics Martin Morgan
• 2011/09/06 Re: [Bioc-sig-seq] about N statistics wang peter
• 2011/09/06 Re: [Bioc-sig-seq] about N statistics Steve Lianoglou
• 2011/09/06 [Bioc-sig-seq] about N statistics wang peter
• 2011/09/06 Re: [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Zhu, Lihua (Julie)
• 2011/09/05 Re: [Bioc-sig-seq] who have RNA-seq pipeline code Steve Lianoglou
• 2011/09/05 Re: [Bioc-sig-seq] who have RNA-seq pipeline code wang peter
• 2011/09/02 Re: [Bioc-sig-seq] who have RNA-seq pipeline code Martin Morgan
• 2011/09/02 Re: [Bioc-sig-seq] a question wang peter
• 2011/09/02 Re: [Bioc-sig-seq] a question Joseph Scandura
• 2011/09/02 [Bioc-sig-seq] who have RNA-seq pipeline code wang peter
• 2011/09/02 Re: [Bioc-sig-seq] a question Martin Morgan
• 2011/09/02 [Bioc-sig-seq] a question wang peter
• 2011/09/02 Re: [Bioc-sig-seq] gaoshan wang peter
• 2011/09/02 Re: [Bioc-sig-seq] gaoshan Sean Davis
• 2011/09/02 [Bioc-sig-seq] gaoshan wang peter
• 2011/09/01 Re: [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Zhu, Lihua (Julie)
• 2011/09/01 Re: [Bioc-sig-seq] using Cuffdiff with biological replicates Jane Merlevede
• 2011/09/01 Re: [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Ou, Jianhong
• 2011/09/01 Re: [Bioc-sig-seq] using Cuffdiff with biological replicates Martin Morgan
• 2011/09/01 [Bioc-sig-seq] using Cuffdiff with biological replicates Jane Merlevede
• 2011/09/01 Re: [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Sonia Leach
• 2011/09/01 Re: [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Ou, Jianhong
• 2011/08/31 [Bioc-sig-seq] edgeR glmLRT contrast Argument Gordon K Smyth
• 2011/08/31 Re: [Bioc-sig-seq] a question about trimLRPatterns Harris A. Jaffee
• 2011/08/31 [Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2 Sonia Leach
• 2011/08/31 Re: [Bioc-sig-seq] a question about trimLRPatterns wang peter
• 2011/08/31 Re: [Bioc-sig-seq] a question about trimLRPatterns Harris A. Jaffee
• 2011/08/30 [Bioc-sig-seq] edgeR glmLRT contrast Argument Dario Strbenac
• 2011/08/30 Re: [Bioc-sig-seq] a question about trimLRPatterns Harris A. Jaffee
• 2011/08/30 Re: [Bioc-sig-seq] import.bw to Rle? [re-opened] Michael Lawrence
• 2011/08/30 [Bioc-sig-seq] a question about trimLRPatterns wang peter
• 2011/08/30 [Bioc-sig-seq] import.bw to Rle? [re-opened] Cook, Malcolm
• 2011/08/29 Re: [Bioc-sig-seq] extract non-zero rows Davis McCarthy
• 2011/08/29 Re: [Bioc-sig-seq] extract non-zero rows Estefania Mancini
• 2011/08/28 Re: [Bioc-sig-seq] extract non-zero rows Dario Strbenac
• 2011/08/25 Re: [Bioc-sig-seq] extract non-zero rows Dario Strbenac
• 2011/08/25 [Bioc-sig-seq] extract non-zero rows Estefania Mancini
• 2011/08/22 [Bioc-sig-seq] HPC/Linux Systems Administrator Position Thomas Girke
• 2011/08/17 Re: [Bioc-sig-seq] using DEXSeq for up and down regulated exons Dario Strbenac
• 2011/08/17 Re: [Bioc-sig-seq] using DEXSeq for up and down regulated exons Jane Merlevede
• 2011/08/12 Re: [Bioc-sig-seq] edgeR datasets Davis McCarthy
• 2011/08/11 Re: [Bioc-sig-seq] assess how many duplicated reads Thomas Girke
• 2011/08/11 Re: [Bioc-sig-seq] assess how many duplicated reads Martin Morgan
• 2011/08/11 Re: [Bioc-sig-seq] edgeR datasets Guffanti Alessandro
• 2011/08/11 [Bioc-sig-seq] edgeR datasets Jérôme Laroche
• 2011/08/11 Re: [Bioc-sig-seq] assess how many duplicated reads Sean Davis
• 2011/08/11 [Bioc-sig-seq] assess how many duplicated reads Kunbin Qu
• 2011/08/10 Re: [Bioc-sig-seq] psetdiff on GRangesLists Error Hervé Pagès
• 2011/08/09 Re: [Bioc-sig-seq] edgeR/454 Davis McCarthy
• 2011/08/09 Re: [Bioc-sig-seq] edgeR/454 Mark Robinson
• 2011/08/09 [Bioc-sig-seq] edgeR/454 Estefania Mancini
• 2011/08/08 Re: [Bioc-sig-seq] problem when using DEXSeq on genes with 1 exon only Simon Anders
• 2011/08/08 Re: [Bioc-sig-seq] problem when using DEXSeq on genes with 1 exon only Wolfgang Huber
• 2011/08/07 Re: [Bioc-sig-seq] using DEXSeq for up and down regulated exons Wolfgang Huber
• 2011/08/03 Re: [Bioc-sig-seq] GRangesList with duplicate names - WORKAROUND Hervé Pagès
• 2011/08/03 [Bioc-sig-seq] using DEXSeq for up and down regulated exons Jane Merlevede
• 2011/08/03 [Bioc-sig-seq] problem when using DEXSeq on genes with 1 exon only Jane Merlevede
• 2011/08/03 Re: [Bioc-sig-seq] GRangesList with duplicate names - WORKAROUND Cook, Malcolm
• 2011/08/03 Re: [Bioc-sig-seq] GRangesList with duplicate names - WORKAROUND Cook, Malcolm
• 2011/07/26 Re: [Bioc-sig-seq] DESeq Nicolas Delhomme
• 2011/07/26 [Bioc-sig-seq] DESeq Bogdan Tanasa
• 2011/07/26 Re: [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Hervé Pagès
• 2011/07/26 Re: [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Kasper Daniel Hansen
• 2011/07/26 Re: [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Martin Morgan
• 2011/07/26 Re: [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Ivan Gregoretti
• 2011/07/26 Re: [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Hervé Pagès
• 2011/07/25 [Bioc-sig-seq] rtracklayer compilation error (make: *** [chain_io.o] Error 1) Ivan Gregoretti
• 2011/07/25 Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Jane Merlevede
• 2011/07/25 Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Jane Merlevede
• 2011/07/25 Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Martin Morgan
• 2011/07/25 Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Martin Morgan
• 2011/07/24 Re: [Bioc-sig-seq] differential binding Mark Robinson
• 2011/07/24 [Bioc-sig-seq] differential binding Bogdan Tanasa
• 2011/07/23 Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Martin Morgan
• 2011/07/23 Re: [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Sean Davis
• 2011/07/23 Re: [Bioc-sig-seq] count the coverage base by base Michael Lawrence
• 2011/07/22 Re: [Bioc-sig-seq] count the coverage base by base Kunbin Qu
• 2011/07/22 Re: [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Gordon K Smyth
• 2011/07/22 Re: [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Gordon K Smyth
• 2011/07/22 Re: [Bioc-sig-seq] count the coverage base by base Kunbin Qu
• 2011/07/22 Re: [Bioc-sig-seq] count the coverage base by base Michael Lawrence
• 2011/07/22 Re: [Bioc-sig-seq] count the coverage base by base Kunbin Qu
• 2011/07/22 Re: [Bioc-sig-seq] count the coverage base by base Michael Lawrence
• 2011/07/22 Re: [Bioc-sig-seq] count the coverage base by base Kunbin Qu
• 2011/07/22 Re: [Bioc-sig-seq] count the coverage base by base Michael Lawrence
• 2011/07/22 [Bioc-sig-seq] count the coverage base by base Kunbin Qu
• 2011/07/22 Re: [Bioc-sig-seq] scanBam memory issue Martin Morgan
• 2011/07/22 Re: [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Sean Ruddy
• 2011/07/22 Re: [Bioc-sig-seq] scanBam memory issue Steve Lianoglou
• 2011/07/22 Re: [Bioc-sig-seq] minoverlap error in countOverlaps Steve Lianoglou
• 2011/07/22 [Bioc-sig-seq] scanBam memory issue Francesco Lescai
• 2011/07/22 [Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux Jane Merlevede
• 2011/07/22 Re: [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Kasper Daniel Hansen
• 2011/07/22 Re: [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Sean Ruddy
• 2011/07/21 [Bioc-sig-seq] minoverlap error in countOverlaps Kunbin Qu
• 2011/07/21 Re: [Bioc-sig-seq] extract gene symbol error Steve Lianoglou
• 2011/07/21 [Bioc-sig-seq] extract gene symbol error Kunbin Qu
• 2011/07/21 [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Gordon K Smyth
• 2011/07/20 [Bioc-sig-seq] psetdiff on GRangesLists Error Dario Strbenac
• 2011/07/20 [Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp Sean Ruddy
• 2011/07/20 Re: [Bioc-sig-seq] reduce in ShortRead Kasper Daniel Hansen
• 2011/07/20 [Bioc-sig-seq] reduce in ShortRead Kunbin Qu
• 2011/07/18 Re: [Bioc-sig-seq] "pooled" dispersion estimation in edgeR Sean Ruddy
• 2011/07/18 Re: [Bioc-sig-seq] "pooled" dispersion estimation in edgeR Gordon K Smyth
• 2011/07/18 Re: [Bioc-sig-seq] "pooled" dispersion estimation in edgeR Sean Ruddy
• 2011/07/18 Re: [Bioc-sig-seq] Supplying own variance functions and adjusted counts to a DESeq dataset Simon Anders
• 2011/07/16 Re: [Bioc-sig-seq] scanBam segfault Ivan Gregoretti
• 2011/07/16 Re: [Bioc-sig-seq] scanBam segfault Martin Morgan
• 2011/07/16 Re: [Bioc-sig-seq] Supplying own variance functions and adjusted counts to a DESeq dataset Simon Anders
• 2011/07/15 [Bioc-sig-seq] "pooled" dispersion estimation in edgeR Gordon K Smyth
• 2011/07/15 Re: [Bioc-sig-seq] Supplying own variance functions and adjusted counts to a DESeq dataset Sean Ruddy
• 2011/07/15 Re: [Bioc-sig-seq] scanBam segfault Martin Morgan
• 2011/07/15 [Bioc-sig-seq] Supplying own variance functions and adjusted counts to a DESeq dataset Gordon K Smyth
• 2011/07/14 Re: [Bioc-sig-seq] using GenomicFeatures Michael Lawrence
• 2011/07/14 Re: [Bioc-sig-seq] Loading large BAM files Martin Morgan
• 2011/07/14 [Bioc-sig-seq] scanBam segfault Ivan Gregoretti
• 2011/07/14 [Bioc-sig-seq] Supplying own variance functions and adjusted counts to a DESeq dataset Sean Ruddy
• 2011/07/14 [Bioc-sig-seq] using GenomicFeatures Jason Lu
• 2011/07/14 Re: [Bioc-sig-seq] Loading large BAM files Ivan Gregoretti
• 2011/07/13 Re: [Bioc-sig-seq] Loading large BAM files Ivan Gregoretti

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