bioc-sig-sequencing  

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• • Re: [Bioc-sig-seq] flank vs shift behaviour on GRanges objects Aaron Statham
  • Re: [Bioc-sig-seq] flank vs shift behaviour on GRanges objects Valerie Obenchain
• [Bioc-sig-seq] ShortRead qa() no longer working Dario Strbenac
  • Re: [Bioc-sig-seq] ShortRead qa() no longer working Martin Morgan
  • Re: [Bioc-sig-seq] ShortRead qa() no longer working Dario Strbenac
  • Re: [Bioc-sig-seq] ShortRead qa() no longer working Martin Morgan
• [Bioc-sig-seq] adding columns to values of GenomicRange objects Jiang, Lichun (NIH/NIDDK) [F]
  • Re: [Bioc-sig-seq] adding columns to values of GenomicRange objects Steve Lianoglou
  • Re: [Bioc-sig-seq] adding columns to values of GenomicRange objects Jiang, Lichun (NIH/NIDDK) [F]
• [Bioc-sig-seq] subsetting a DNAStringSet Andrew Yee
  • Re: [Bioc-sig-seq] subsetting a DNAStringSet Martin Morgan
  • Re: [Bioc-sig-seq] subsetting a DNAStringSet Andrew Yee
• [Bioc-sig-seq] findOverlaps Documented Option Dario Strbenac
  • Re: [Bioc-sig-seq] findOverlaps Documented Option Martin Morgan
  • Re: [Bioc-sig-seq] findOverlaps Documented Option Michael Lawrence
• [Bioc-sig-seq] findOverlaps minoverlap Dario Strbenac
• [Bioc-sig-seq] read length distribution from ShortReadQ or AlignedRead joseph
  • Re: [Bioc-sig-seq] read length distribution from ShortReadQ or AlignedRead Steve Lianoglou
  • Re: [Bioc-sig-seq] read length distribution from ShortReadQ or AlignedRead Steve Lianoglou
  • Re: [Bioc-sig-seq] read length distribution from ShortReadQ or AlignedRead joseph
  • Re: [Bioc-sig-seq] read length distribution from ShortReadQ or AlignedRead Martin Morgan
  • Re: [Bioc-sig-seq] read length distribution from ShortReadQ or AlignedRead joseph
  • Re: [Bioc-sig-seq] read length distribution from ShortReadQ or AlignedRead Martin Morgan
• [Bioc-sig-seq] coverage vectors and subseq kirti prakash
  • Re: [Bioc-sig-seq] coverage vectors and subseq Martin Morgan
  • Re: [Bioc-sig-seq] coverage vectors and subseq kirti prakash
  • Re: [Bioc-sig-seq] coverage vectors and subseq Martin Morgan
  • Re: [Bioc-sig-seq] coverage vectors and subseq kirti prakash
  • Re: [Bioc-sig-seq] coverage vectors and subseq kirti prakash
• [Bioc-sig-seq] trimLRPatterns - adaptor trimming JASREET HUNDAL
  • Re: [Bioc-sig-seq] trimLRPatterns - adaptor trimming Marcus Davy
  • Re: [Bioc-sig-seq] trimLRPatterns - adaptor trimming JASREET HUNDAL
  • Re: [Bioc-sig-seq] trimLRPatterns - adaptor trimming Martin Morgan
  • Re: [Bioc-sig-seq] trimLRPatterns - adaptor trimming Harris A. Jaffee
  • Re: [Bioc-sig-seq] trimLRPatterns - adaptor trimming Martin Morgan
  • Re: [Bioc-sig-seq] trimLRPatterns - adaptor trimming JASREET HUNDAL
  • Re: [Bioc-sig-seq] trimLRPatterns - adaptor trimming Steve Lianoglou
  • Re: [Bioc-sig-seq] trimLRPatterns - adaptor trimming Martin Morgan
  • Re: [Bioc-sig-seq] trimLRPatterns - adaptor trimming JASREET HUNDAL
• [Bioc-sig-seq] Implementing workflow.pdf (BioC2010 lab handout) [email protected]
  • Re: [Bioc-sig-seq] Implementing workflow.pdf (BioC2010 lab handout) Michael Lawrence
• [Bioc-sig-seq] overlaying coverage plots LU Zen
  • Re: [Bioc-sig-seq] overlaying coverage plots Martin Morgan
  • Re: [Bioc-sig-seq] overlaying coverage plots LU Zen
  • Re: [Bioc-sig-seq] overlaying coverage plots Martin Morgan
  • Re: [Bioc-sig-seq] overlaying coverage plots LU Zen
  • Re: [Bioc-sig-seq] overlaying coverage plots Wolfgang Huber
• [Bioc-sig-seq] Converting SimpleRleViewsList to SimpleRleList Johannes Waage
  • Re: [Bioc-sig-seq] Converting SimpleRleViewsList to SimpleRleList Michael Lawrence
• [Bioc-sig-seq] Problem compiling Rsamtools 1.0.7 Lapointe, David
  • Re: [Bioc-sig-seq] Problem compiling Rsamtools 1.0.7 Martin Morgan
• [Bioc-sig-seq] Counting mismatches with vmatchPattern Marcus Davy
  • Re: [Bioc-sig-seq] Counting mismatches with vmatchPattern Hervé Pagès
  • Re: [Bioc-sig-seq] Counting mismatches with vmatchPattern Marcus Davy
• [Bioc-sig-seq] rtracklayer - suppress track line Chris Seidel
  • Re: [Bioc-sig-seq] rtracklayer - suppress track line Chris Seidel
  • Re: [Bioc-sig-seq] rtracklayer - suppress track line Michael Lawrence
• [Bioc-sig-seq] GRanges tabulate the coverage Dario Strbenac
  • Re: [Bioc-sig-seq] GRanges tabulate the coverage Patrick Aboyoun
  • Re: [Bioc-sig-seq] GRanges tabulate the coverage Patrick Aboyoun
• [Bioc-sig-seq] GRanges resize Behaviour Dario Strbenac
  • Re: [Bioc-sig-seq] GRanges resize Behaviour Patrick Aboyoun
• [Bioc-sig-seq] rtracklayer and import()ing into GRanges Ivan Gregoretti
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Michael Lawrence
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Ivan Gregoretti
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Patrick Aboyoun
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Michael Lawrence
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Patrick Aboyoun
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Michael Lawrence
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Patrick Aboyoun
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Michael Lawrence
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Patrick Aboyoun
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Ivan Gregoretti
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Ivan Gregoretti
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Ivan Gregoretti
  • Re: [Bioc-sig-seq] rtracklayer and import()ing into GRanges Ivan Gregoretti
• [Bioc-sig-seq] PairwiseAlignedXStringSet to PairwiseAlignedFixedSubject Stefan Bentink
  • Re: [Bioc-sig-seq] PairwiseAlignedXStringSet to PairwiseAlignedFixedSubject Kasper Daniel Hansen
  • Re: [Bioc-sig-seq] PairwiseAlignedXStringSet to PairwiseAlignedFixedSubject Patrick Aboyoun
  • Re: [Bioc-sig-seq] PairwiseAlignedXStringSet to PairwiseAlignedFixedSubject Stefan Bentink
  • Re: [Bioc-sig-seq] PairwiseAlignedXStringSet to PairwiseAlignedFixedSubject Patrick Aboyoun
  • Re: [Bioc-sig-seq] PairwiseAlignedXStringSet to PairwiseAlignedFixedSubject Stefan Bentink
• [Bioc-sig-seq] Suggest enhancement in GRanges: add method setAs("Granges", "IntervalTree") Steve Lianoglou
  • Re: [Bioc-sig-seq] Suggest enhancement in GRanges: add method setAs("Granges", "IntervalTree") Michael Lawrence
  • Re: [Bioc-sig-seq] Suggest enhancement in GRanges: add method setAs("Granges", "IntervalTree") Steve Lianoglou
  • Re: [Bioc-sig-seq] Suggest enhancement in GRanges: add method setAs("Granges", "IntervalTree") Michael Lawrence
• [Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)? Steve Lianoglou
  • Re: [Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)? Steve Lianoglou
  • Re: [Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)? Patrick Aboyoun
  • Re: [Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)? Marc Carlson
  • Re: [Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)? Patrick Aboyoun
  • Re: [Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)? Patrick Aboyoun
  • Re: [Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)? Hervé Pagès
  • Re: [Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)? Steve Lianoglou
  • Re: [Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)? Hervé Pagès
  • Re: [Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)? Steve Lianoglou
  • Re: [Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)? Hervé Pagès
• [Bioc-sig-seq] There is a bug living in Rsamtools_1.0.6:::.io_bam codepath. Steve Lianoglou
  • Re: [Bioc-sig-seq] There is a bug living in Rsamtools_1.0.6:::.io_bam codepath. Martin Morgan
  • [Bioc-sig-seq] Thanks for organizing BioC2010 Pratap, Abhishek
• [Bioc-sig-seq] Applying grep to a large number of tags. (looking for speed) Ivan Gregoretti
  • Re: [Bioc-sig-seq] Applying grep to a large number of tags. (looking for speed) Patrick Aboyoun
  • Re: [Bioc-sig-seq] Applying grep to a large number of tags. (looking for speed) Patrick Aboyoun
  • Re: [Bioc-sig-seq] Applying grep to a large number of tags. (looking for speed) Ivan Gregoretti
  • Re: [Bioc-sig-seq] Applying grep to a large number of tags. (looking for speed) Patrick Aboyoun
  • Re: [Bioc-sig-seq] Applying grep to a large number of tags. (looking for speed) Ivan Gregoretti
  • Re: [Bioc-sig-seq] Applying grep to a large number of tags. (looking for speed) Patrick Aboyoun
  • Re: [Bioc-sig-seq] Applying grep to a large number of tags. (looking for speed) Ivan Gregoretti
  • Re: [Bioc-sig-seq] Applying grep to a large number of tags. (looking for speed) Cei Abreu-Goodger
• [Bioc-sig-seq] Open Postdoc Positions Thomas Girke
  • [Bioc-sig-seq] Open Postdoc Positions Thomas Girke
• [Bioc-sig-seq] ChIPseqR question Robert Morris
  • Re: [Bioc-sig-seq] ChIPseqR question Hervé Pagès
• [Bioc-sig-seq] Coercion of GenomeData to RangedData Dario Strbenac
  • Re: [Bioc-sig-seq] Coercion of GenomeData to RangedData Michael Lawrence
  • [Bioc-sig-seq] Coercion of GenomeData to RangedData Dario Strbenac
  • Re: [Bioc-sig-seq] Coercion of GenomeData to RangedData Vincent Carey
  • Re: [Bioc-sig-seq] Coercion of GenomeData to RangedData Dario Strbenac
  • Re: [Bioc-sig-seq] Coercion of GenomeData to RangedData Michael Lawrence
  • Re: [Bioc-sig-seq] Coercion of GenomeData to RangedData Dario Strbenac
  • Re: [Bioc-sig-seq] Coercion of GenomeData to RangedData Michael Lawrence
• [Bioc-sig-seq] using subseq() in Biostrings to insert bases Andrew Yee
  • Re: [Bioc-sig-seq] using subseq() in Biostrings to insert bases Michael Lawrence
  • Re: [Bioc-sig-seq] using subseq() in Biostrings to insert bases Vincent Carey
  • Re: [Bioc-sig-seq] using subseq() in Biostrings to insert bases Andrew Yee
  • Re: [Bioc-sig-seq] using subseq() in Biostrings to insert bases Hervé Pagès
  • Re: [Bioc-sig-seq] using subseq() in Biostrings to insert bases Andrew Yee
• [Bioc-sig-seq] Downloading a sequence from the NCBI Ivan Gregoretti
  • Re: [Bioc-sig-seq] Downloading a sequence from the NCBI Martin Morgan
  • Re: [Bioc-sig-seq] Downloading a sequence from the NCBI Ivan Gregoretti
• [Bioc-sig-seq] Equalize number reads before chipseq analysis [email protected]
• [Bioc-sig-seq] GRanges, ordering and subsetting Ivan Gregoretti
  • Re: [Bioc-sig-seq] GRanges, ordering and subsetting Steve Lianoglou
  • Re: [Bioc-sig-seq] GRanges, ordering and subsetting Ivan Gregoretti
  • Re: [Bioc-sig-seq] GRanges, ordering and subsetting Martin Morgan
  • [Bioc-sig-seq] How to convert upper case strings to lower case xuxiang086
  • Re: [Bioc-sig-seq] How to convert upper case strings to lower case Cei Abreu-Goodger
  • Re: [Bioc-sig-seq] How to convert upper case strings to low er case xuxiang086
  • Re: [Bioc-sig-seq] How to convert upper case strings to lower case Joern Toedling
• [Bioc-sig-seq] mappable length of a genome Cei Abreu-Goodger
  • Re: [Bioc-sig-seq] mappable length of a genome Kasper Daniel Hansen
  • Re: [Bioc-sig-seq] mappable length of a genome Cei Abreu-Goodger
• [Bioc-sig-seq] Alignment to only 1 direction DNA strand Lana Schaffer
  • Re: [Bioc-sig-seq] Alignment to only 1 direction DNA strand Steve Lianoglou
• Re: [Bioc-sig-seq] Bioc-sig-sequencing Digest, Vol 28, Issue 30 Lana Schaffer
  • Re: [Bioc-sig-seq] Bioc-sig-sequencing Digest, Vol 28, Issue 30 Kasper Daniel Hansen
• [Bioc-sig-seq] findOverlaps fails when querying a RangedData/RangesList against itself Aaron Statham
  • Re: [Bioc-sig-seq] findOverlaps fails when querying a RangedData/RangesList against itself Michael Lawrence
• [Bioc-sig-seq] GenomicRanges: accessing coverage data in output of Views() ? Daniela Drechsel
  • Re: [Bioc-sig-seq] GenomicRanges: accessing coverage data in output of Views() ? Michael Lawrence
• [Bioc-sig-seq] Semantics of strandedness for gaps function Dario Strbenac
  • Re: [Bioc-sig-seq] Semantics of strandedness for gaps function Patrick Aboyoun
• [Bioc-sig-seq] matchPDict, fixed=FALSE; "walk_tb_nonfixed_subject(): implement me" Ludo Pagie
  • Re: [Bioc-sig-seq] matchPDict, fixed=FALSE; "walk_tb_nonfixed_subject(): implement me" Hervé Pagès
  • Re: [Bioc-sig-seq] matchPDict, fixed=FALSE; "walk_tb_nonfixed_subject(): implement me" Hervé Pagès
  • Re: [Bioc-sig-seq] matchPDict, fixed=FALSE; "walk_tb_nonfixed_subject(): implement me" Hervé Pagès
• [Bioc-sig-seq] Finding Mean Value of Overlapping Ranges Dario Strbenac
  • Re: [Bioc-sig-seq] Finding Mean Value of Overlapping Ranges Michael Lawrence
  • Re: [Bioc-sig-seq] Finding Mean Value of Overlapping Ranges Dario Strbenac
  • Re: [Bioc-sig-seq] Finding Mean Value of Overlapping Ranges Hervé Pagès
  • Re: [Bioc-sig-seq] Finding Mean Value of Overlapping Ranges Dario Strbenac
• [Bioc-sig-seq] coverage() in IRanges Andrew Yee
  • Re: [Bioc-sig-seq] coverage() in IRanges Martin Morgan
  • Re: [Bioc-sig-seq] coverage() in IRanges Andrew Yee
  • Re: [Bioc-sig-seq] coverage() in IRanges Hervé Pagès
  • Re: [Bioc-sig-seq] coverage() in IRanges Andrew Yee
  • Re: [Bioc-sig-seq] coverage() in IRanges Hervé Pagès
  • Re: [Bioc-sig-seq] coverage() in IRanges Andrew Yee
• [Bioc-sig-seq] Local Context James Bullard
  • [Bioc-sig-seq] Local Context James Bullard
  • Re: [Bioc-sig-seq] Local Context Patrick Aboyoun
  • Re: [Bioc-sig-seq] Local Context Hervé Pagès
• [Bioc-sig-seq] Accessing range values from Rle object [email protected]
  • Re: [Bioc-sig-seq] Accessing range values from Rle object Patrick Aboyoun
• [Bioc-sig-seq] stringDist; hamming Ludo Pagie
  • Re: [Bioc-sig-seq] stringDist; hamming Patrick Aboyoun
• [Bioc-sig-seq] Memory bottlenecks while using ShortRead Cei Abreu-Goodger
  • Re: [Bioc-sig-seq] Memory bottlenecks while using ShortRead Martin Morgan
  • Re: [Bioc-sig-seq] Memory bottlenecks while using ShortRead Steve Lianoglou
• Re: [Bioc-sig-seq] questions on Coverage function and IRanges package Patrick Aboyoun
  • Re: [Bioc-sig-seq] questions on Coverage function and IRanges package Di, Xiaojun
  • Re: [Bioc-sig-seq] questions on Coverage function and IRanges package Di, Xiaojun
• [Bioc-sig-seq] Process for ChIP-seq FDR determination (followup) [email protected]
  • Re: [Bioc-sig-seq] Process for ChIP-seq FDR determination (followup) Michael Lawrence
• [Bioc-sig-seq] GenomicRanges findOverlaps error message Dario Strbenac
  • Re: [Bioc-sig-seq] GenomicRanges findOverlaps error message Michael Lawrence
• [Bioc-sig-seq] Process for ChIP-seq FDR determination [email protected]
  • Re: [Bioc-sig-seq] Process for ChIP-seq FDR determination Michael Lawrence
• [Bioc-sig-seq] BioC 2010 Conference Update Martin Morgan
• [Bioc-sig-seq] Browser display question (clarification) [email protected]
  • Re: [Bioc-sig-seq] Browser display question (clarification) Michael Lawrence
• [Bioc-sig-seq] getting integers from SimpleRleViewsList Janet Young
  • Re: [Bioc-sig-seq] getting integers from SimpleRleViewsList Michael Lawrence
  • Re: [Bioc-sig-seq] getting integers from SimpleRleViewsList Janet Young
  • [Bioc-sig-seq] seqselect on SimpleRleList and RangesList - bug? and request Janet Young
  • Re: [Bioc-sig-seq] seqselect on SimpleRleList and RangesList - bug? and request Patrick Aboyoun
  • Re: [Bioc-sig-seq] seqselect on SimpleRleList and RangesList - bug? and request Michael Lawrence
  • Re: [Bioc-sig-seq] seqselect on SimpleRleList and RangesList - bug? and request Patrick Aboyoun
  • Re: [Bioc-sig-seq] seqselect on SimpleRleList and RangesList - bug? and request Janet Young
  • Re: [Bioc-sig-seq] seqselect on SimpleRleList and RangesList - bug? and request Michael Lawrence

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