February 2013 Archives by author
Starting: Fri Feb 1 00:07:18 CET 2013
Ending: Thu Feb 28 23:51:58 CET 2013
Messages: 524
- [BioC] Required Annotation Package for Agilent-021974
Ahmad
- [BioC] how to supply a vector/list of results to GenTable in topGO?
Adrian Alexa
- [BioC] Student Internships at Illumina Cambridge Ltd.
Adrian Alexa
- [BioC] Student Internships at Illumina Cambridge Ltd.
Adrian Alexa
- [BioC] subset GRanges object via ElementMetadata
Arnaud Amzallag
- [BioC] Getting DESEq results on just one gene
Simon Anders
- [BioC] DESeq Design issue
Simon Anders
- [BioC] EBImage: putting two images next to each others
Simon Anders
- [BioC] EBImage: putting two images next to each others
Simon Anders
- [BioC] DEXSeq dexseq_prepare_annotation.py error
Simon Anders
- [BioC] easyRNA adapting annotations to avoid overlapping synthetic exons
Bayles, Darrell
- [BioC] Rtracklayer and track/table names
Gustavo Fernández Bayón
- [BioC] Rtracklayer and track/table names
Gustavo Fernández Bayón
- [BioC] Detecting significant trends in variability
Gustavo Fernández Bayón
- [BioC] DataFrame bug?
Charles Berry
- [BioC] Aligning short reads to a single gene
Ugo Borello
- [BioC] DiffBind error loading dba.count
Gordon Brown
- [BioC] filtering Gene 1.0 ST chips
Dennis Burian
- [BioC] easyRNASeq read counts varying when recounting same sample!
René Böttcher
- [BioC] pileup coverage from BAM file
Chris Cabanski
- [BioC] plotting BED intervals to TSS regions
Jonathan Cairns
- [BioC] DEXseq: several "1" and "NA" in padjust column
Vincenzo Capece
- [BioC] DEXseq: several "1" and "NA" in padjust column
Vincenzo Capece
- [BioC] DEXseq: several "1" and "NA" in padjust column
Vincenzo Capece
- [BioC] Issues while installing RBGL package
Vincent Carey
- [BioC] Issues while installing RBGL package
Vincent Carey
- [BioC] Boston Bioconductor Basics, April 4-5 2013
Vincent Carey
- [BioC] qvalue pi0 computation
Vincent Carey
- [BioC] annotation for Agilent Mouse an d Human 8x60K array
Marc Carlson
- [BioC] Gene Ontologies exploration
Marc Carlson
- [BioC] (missing?) UCSCKG -> SYMBOL mappings in Homo.sapiens (etc.)
Marc Carlson
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Marc Carlson
- [BioC] Building a TranscriptDb object from a lncRNA gft file
Marc Carlson
- [BioC] How to make a db package for Agilent-015354 Bovine Oligo Microarray (4x44K)?
Marc Carlson
- [BioC] Error in sqliteExecStatement(con, statement, bind.data)
Marc Carlson
- [BioC] DEXSeq package - read.HTSeqCount function error
Matteo Carrara
- [BioC] problem with pd.huex.1.0.st.v2 and oligo::getProbeInfo
Benilton Carvalho
- [BioC] graph::subGraph() problem with node attributes
Robert Castelo
- [BioC] GSVA error
Robert Castelo
- [BioC] =?x-gbk?Q?=BB=D8=B8=B4=3ARe=3A_=5BBioC=5D_GSVA_error?=
Robert Castelo
- [BioC] Question: GSVA error
Robert Castelo
- [BioC] bug in graph::edgeData()
Robert Castelo
- [BioC] bug in graph::edgeData()
Robert Castelo
- [BioC] bug in graph::edgeData()
Robert Castelo
- [BioC] GSVA
Robert Castelo
- [BioC] GSVA
Robert Castelo
- [BioC] Getting DESEq results on just one gene
Fong Chun Chan
- [BioC] Getting DESEq results on just one gene
Fong Chun Chan
- [BioC] Getting Introns Expression at a Per Gene Level
Fong Chun Chan
- [BioC] Getting Introns Expression at a Per Gene Level
Fong Chun Chan
- [BioC] Detecting differential usage of introns from RNA-seq data.
Fong Chun Chan
- [BioC] Detecting differential usage of introns from RNA-seq data.
Fong Chun Chan
- [BioC] Detecting differential usage of introns from RNA-seq data.
Fong Chun Chan
- [BioC] Detecting differential usage of introns from RNA-seq data.
Fong Chun Chan
- [BioC] Building a TranscriptDb object from a lncRNA gft file
Fong Chun Chan
- [BioC] MEDIPS
Lukas Chavez
- [BioC] Fwd: Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Lukas Chavez
- [BioC] Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Lukas Chavez
- [BioC] Job openings at Barts Cancer Institute, QMUL: Postdoctoral Research assistant and Bioinformatician
Claude Chelala
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Kaj Chokeshaiusaha
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Kaj Chokeshaiusaha
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Kaj Chokeshaiusaha
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Kaj Chokeshaiusaha
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Kaj Chokeshaiusaha
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Kaj Chokeshaiusaha
- [BioC] How to make a db package for Agilent-015354 Bovine Oligo Microarray (4x44K)?
Kaj Chokeshaiusaha
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Kaj Chokeshaiusaha
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Kaj Chokeshaiusaha
- [BioC] Filtering out tags with low counts in edgeR results in fewer differentially expressed genes.....
Mark Christie
- [BioC] Filtering out tags with low counts in edgeR results in fewer differentially expressed genes.....
Mark Christie
- [BioC] What does this mean in Limma?
Davide Cittaro
- [BioC] What does this mean in Limma?
Davide Cittaro
- [BioC] limma-voom and y$E
Davide Cittaro
- [BioC] statistical test for time course data
Davide Cittaro
- [BioC] statistical test for time course data
Davide Cittaro
- [BioC] edgeR: counts or pseudo.counts?
Davide Cittaro
- [BioC] Generalized edgeR functions
Davide Cittaro
- [BioC] edgeR: counts or pseudo.counts?
Davide Cittaro
- [BioC] Reminder - VIB Nucleomics Core - User Meeting 2013
VIB Nucleomics Core
- [BioC] filtering Gene 1.0 ST chips
Mark Cowley
- [BioC] Simple question about Vector
Mark Cowley
- [BioC] merging of Affy U133A and U133B
Philippe DESSEN
- [BioC] Trouble creating a ShortReadQ object and using writeFastq
NOAH LEE DOWELL
- [BioC] useDevel() not working
Jahn Davik
- [BioC] merging of Affy U133A and U133B
Sean Davis
- [BioC] easyRNASeq read counts varying when recounting same sample!
Nicolas Delhomme
- [BioC] DiffBind - Scores for peakset are all the same
António Domingues
- [BioC] DiffBind - Scores for peakset are all the same
António Domingues
- [BioC] Trouble creating a ShortReadQ object and using writeFastq
Noah Dowell
- [BioC] Sorry for cross post: Trouble creating ShortReadQ object and using writeFastq
Noah Dowell
- [BioC] genoset:::initGenoSet
Pan Du
- [BioC] Extract microarray data for genes identified by GO analysis
Mark Ebbert
- [BioC] Extract microarray data for genes identified by GO analysis
Mark Ebbert
- [BioC] Extract microarray data for genes identified by GO analysis
Mark Ebbert
- [BioC] ComBat: sample of files to use in ComBat.R
Edwin
- [BioC] rhdf5 and factors
Stephen Eglen
- [BioC] XPS: Arabidopsis Gene 1.0 ST Array, import.exon.scheme ERROR
Motomu Endo
- [BioC] XPS: Arabidopsis Gene 1.0 ST Array, import.exon.scheme ERROR
Motomu Endo
- [BioC] runSPIA() in graphite package
Enrica
- [BioC] runSPIA() in graphite package
Enrica
- [BioC] edgeR choose the best model of GLM
Ari Eszter
- [BioC] edgeR choose the best model of GLM
Ari Eszter
- [BioC] annotation for Agilent Mouse an d Human 8x60K array
Marco Fabbri
- [BioC] Package DRC: multiple treatment groups
Hendrik Falk
- [BioC] Difference between number of probes and number of data rows using 'oligo' on Affy miRNA v3.0 arrays
Vicky Fan
- [BioC] gage: essGene()
Forst, Christian
- [BioC] statistical test for time course data
Richard Friedman
- [BioC] statistical test for time course data
Richard Friedman
- [BioC] statistical test for time course data
Richard Friedman
- [BioC] statistical test for time course data
Richard Friedman
- [BioC] statistical test for time course data
Richard Friedman
- [BioC] Extracting strand information from GenomicFeatures transcript db objects
Veerendra GP
- [BioC] Extracting strand information from GenomicFeatures transcript db objects
Veerendra GP
- [BioC] statistical test for time course data
Paul Geeleher
- [BioC] Visualization of alignments with mismatch bases
Julian Gehring
- [BioC] Visualization of alignments with mismatch bases
Julian Gehring
- [BioC] Visualization of alignments with mismatch bases
Julian Gehring
- [BioC] How can I use the information from an ADF [Array Design File] file for microarray normalization?
Christoph Geisenberger
- [BioC] suppressing reduce() function when applying set operations to GRanges
Bill Gibb
- [BioC] HTqPCR problem with creation of qPCRset
Elisabeth Gilis
- [BioC] HTqPCR problem with creation of qPCRset
Elisabeth Gilis
- [BioC] BitSeq: Required input for 3' bias correction on transcripts.
Peter Glaus
- [BioC] merging VCF files
Stephanie M. Gogarten
- [BioC] GWASTools for analyzing Canine_HD genotyping data
Stephanie M. Gogarten
- [BioC] merging VCF files
Stephanie M. Gogarten
- [BioC] Agilent Mouse 8x60K array
Nathan (Nat) Goodman
- [BioC] Agilent Mouse 8x60K array
Nathan (Nat) Goodman
- [BioC] Agilent Mouse 8x60K array
Nathan (Nat) Goodman
- [BioC] Agilent Mouse 8x60K array
Nathan (Nat) Goodman
- [BioC] Agilent Mouse 8x60K array
Nathan (Nat) Goodman
- [BioC] Agilent Mouse 8x60K array
Nathan (Nat) Goodman
- [BioC] Pre-processing and probe removal in lumi
Lavinia Gordon
- [BioC] readFasta and gzipped FASTA files
Ivan Gregoretti
- [BioC] readFasta and gzipped FASTA files
Ivan Gregoretti
- [BioC] readFasta and gzipped FASTA files
Ivan Gregoretti
- [BioC] Fwd: statistical test for time course data
Alex Gutteridge
- [BioC] bsseq and BSmooth with RRBS
Alex Gutteridge
- [BioC] bsseq and BSmooth with RRBS
Alex Gutteridge
- [BioC] Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands
Hahne, Florian
- [BioC] question about Gviz
Hahne, Florian
- [BioC] question about Gviz
Hahne, Florian
- [BioC] Finding closest gene to chromosomal position (non-human or mouse)
Molly Hanlon
- [BioC] Finding closest gene to chromosomal position (non-human or mouse)
Molly Hanlon
- [BioC] statistical test for time course data
Juliet Hannah
- [BioC] Bumphunter output
Kasper Daniel Hansen
- [BioC] R crashes when using CDF package generated using makecdfenv
Kasper Daniel Hansen
- [BioC] Bumphunter output
Kasper Daniel Hansen
- [BioC] using offsets from EDASeq and cqn for edgeR
Kasper Daniel Hansen
- [BioC] bsseq and BSmooth with RRBS
Kasper Daniel Hansen
- [BioC] Bumphunter output
Kasper Daniel Hansen
- [BioC] R crashes when using CDF package generated using makecdfenv
Kasper Daniel Hansen
- [BioC] Log transformation and left censoring
Paul Harrison
- [BioC] Log transformation and left censoring
Paul Harrison
- [BioC] Log transformation and left censoring
Paul Harrison
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Andreas Heider
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Andreas Heider
- [BioC] [devteam-bioc] Rsamtools installation error
Theresa Hodges
- [BioC] annotationTools: character vector clean-up
Hooiveld, Guido
- [BioC] Log transformation and left censoring
Wolfgang Huber
- [BioC] Log transformation and left censoring
Wolfgang Huber
- [BioC] miRNA analysis advice
Fiona Ingleby
- [BioC] miRNA analysis advice
Fiona Ingleby
- [BioC] statistical test for time course data
chris Jhon
- [BioC] statistical test for time course data
chris Jhon
- [BioC] Fwd: statistical test for time course data
chris Jhon
- [BioC] Fwd: statistical test for time course data
chris Jhon
- [BioC] Problems with medianFilter in EBImage 4.0.0
Kent Johnson
- [BioC] ComBat: How to choose multiple covariates in ComBat analysis- Need advice
Johnson, William Evan
- [BioC] qRT-PCR - reading tab-delimited file (biol & tech replicates)
Maciej Jończyk
- [BioC] Design question: How to account for dependent samples?
Moritz Kebschull
- [BioC] AgiMicroRna for new Agilent Chip format - columns gTotalGeneSignal and gTotalProbeSignal missing
Axel Klenk
- [BioC] MEDIPS
Paolo Kunderfranco
- [BioC] MEDIPS
Paolo Kunderfranco
- [BioC] ChIPpeakAnno "examplePattern.fa" file
José Luis Lavín
- [BioC] ChIPpeakAnno "examplePattern.fa" file
José Luis Lavín
- [BioC] Accessing Bioconductor from Java
Michael Lawrence
- [BioC] Rtracklayer and track/table names
Michael Lawrence
- [BioC] rtracklayer weirdness
Michael Lawrence
- [BioC] gmapR/gsnap crashes
Michael Lawrence
- [BioC] subset GRanges object via ElementMetadata
Michael Lawrence
- [BioC] subset GRanges object via ElementMetadata
Michael Lawrence
- [BioC] subset GRanges object via ElementMetadata
Michael Lawrence
- [BioC] Accessing Bioconductor from Java
Steve Lianoglou
- [BioC] DEXSeq package - read.HTSeqCount function error
Steve Lianoglou
- [BioC] Getting DESEq results on just one gene
Steve Lianoglou
- [BioC] DEXseq: several "1" and "NA" in padjust column
Steve Lianoglou
- [BioC] DEXseq: several "1" and "NA" in padjust column
Steve Lianoglou
- [BioC] Gene Ontologies exploration
Steve Lianoglou
- [BioC] statistical test for time course data
Steve Lianoglou
- [BioC] edgeR cpm filtering
Steve Lianoglou
- [BioC] Problem of Ctrl+L in RStudio:
Steve Lianoglou
- [BioC] What happened to GenomicFeatures::spliceGraph?
Steve Lianoglou
- [BioC] subset GRanges object via ElementMetadata
Steve Lianoglou
- [BioC] miRNA analysis advice
Steve Lianoglou
- [BioC] miRNA analysis advice
Steve Lianoglou
- [BioC] illegal operand when I run DEXSeq
Steve Lianoglou
- [BioC] illegal operand when I run DEXSeq
Steve Lianoglou
- [BioC] using offsets from EDASeq and cqn
Michael Love
- [BioC] using offsets from EDASeq and cqn for edgeR
Michael Love
- [BioC] using offsets from EDASeq and cqn
Mike Love
- [BioC] Agilent Mouse 8x60K array
James W. MacDonald
- [BioC] Agilent Mouse 8x60K array
James W. MacDonald
- [BioC] Agilent Mouse 8x60K array
James W. MacDonald
- [BioC] Agilent Mouse 8x60K array
James W. MacDonald
- [BioC] Creating annotation database for GOstat
James W. MacDonald
- [BioC] How to pool subgroups for makeContrasts() and subsequent limma analysis?
James W. MacDonald
- [BioC] problem with GDS2eSet function in GEOquery package
James W. MacDonald
- [BioC] edgeR cpm filtering
James W. MacDonald
- [BioC] distanceToNearest in GenomicRanges
James W. MacDonald
- [BioC] edgeR cpm filtering
James W. MacDonald
- [BioC] Differences in results analyzing Mouse Gene 1.0-ST using oligo and affy package
James W. MacDonald
- [BioC] Differences in results analyzing Mouse Gene 1.0-ST using oligo and affy package
James W. MacDonald
- [BioC] Problem installing packages on new R
James W. MacDonald
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
James W. MacDonald
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
James W. MacDonald
- [BioC] edgeR import error
James W. MacDonald
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
James W. MacDonald
- [BioC] Extract microarray data for genes identified by GO analysis
James W. MacDonald
- [BioC] Retrieving dN, dS from biomaRt fails: Attributes from multiple pages not allowed
James W. MacDonald
- [BioC] Regarding Limma differential expression.
James W. MacDonald
- [BioC] HTqPCR problem with creation of qPCRset
James W. MacDonald
- [BioC] Extract microarray data for genes identified by GO analysis
James W. MacDonald
- [BioC] qvalue pi0 computation
James W. MacDonald
- [BioC] Extract microarray data for genes identified by GO analysis
James W. MacDonald
- [BioC] query on variance parameters for RMA
James W. MacDonald
- [BioC] query on variance parameters for RMA
James W. MacDonald
- [BioC] reading in data in ReadqPCR
James W. MacDonald
- [BioC] Difference between number of probes and number of data rows using 'oligo' on Affy miRNA v3.0 arrays
James W. MacDonald
- [BioC] transform Illumina intensity for heatmap
James W. MacDonald
- [BioC] miRNA analysis advice
James W. MacDonald
- [BioC] query regarding memory allocation...please help
James W. MacDonald
- [BioC] Simple question about Vector
Thiago Maia
- [BioC] Gene Ontologies exploration
Jose M Garcia Manteiga
- [BioC] Bumphunter and minfi
Zilbauer Matthias
- [BioC] Useful information about Ensembl release 70 mart databases
Thomas Maurel
- [BioC] Fwd: iScan
Rajasree Menon
- [BioC] Loading eSet.r objects from ArrayExpress
Mirza, Nasir
- [BioC] Differentially regulated genes
Ali Mohammadian
- [BioC] HiTC: problem with HTClist
Martin Morgan
- [BioC] counting BAM reads in a set of genomic regions
Martin Morgan
- [BioC] readFasta and gzipped FASTA files
Martin Morgan
- [BioC] adding papaya genome to BSgenome
Martin Morgan
- [BioC] where is exonsOnTP53Genome defined
Martin Morgan
- [BioC] New course material: Intermediate R / Bioc for High-Throughput Sequence Analysis
Martin Morgan
- [BioC] Trouble creating a ShortReadQ object and using writeFastq
Martin Morgan
- [BioC] Trouble creating a ShortReadQ object and using writeFastq
Martin Morgan
- [BioC] What happened to GenomicFeatures::spliceGraph?
Martin Morgan
- [BioC] subset GRanges object via ElementMetadata
Martin Morgan
- [BioC] writeFastq writing dashes instead of dots
Martin Morgan
- [BioC] writeFastq writing dashes instead of dots
Martin Morgan
- [BioC] illegal operand when I run DEXSeq
Martin Morgan
- [BioC] CharacerToFASTArecords
Nair, Murlidharan T
- [BioC] CharacerToFASTArecords
Nair, Murlidharan T
- [BioC] HiTC: problem with HTClist
Hermann Norpois
- [BioC] genome_intervals and GRange objects/HiTC package
Hermann Norpois
- [BioC] genome_intervals and GRange objects/HiTC package
Hermann Norpois
- [BioC] Generate a GRangesList from a classical list of GRangesObjects
Hermann Norpois
- [BioC] Generate a GRangesList from a classical list of GRangesObjects
Hermann Norpois
- [BioC] subset GRanges object via ElementMetadata
Hermann Norpois
- [BioC] distanceToNearest in GenomicRanges
Tom Oates
- [BioC] distanceToNearest in GenomicRanges
Tom Oates
- [BioC] ties & strandedness in distanceToNearest GRanges
Tom Oates
- [BioC] transcriptDb object not found when call locateVariants() in a function
Valerie Obenchain
- [BioC] Getting Introns Expression at a Per Gene Level
Valerie Obenchain
- [BioC] graph::subGraph() problem with node attributes
Valerie Obenchain
- [BioC] Getting Introns Expression at a Per Gene Level
Valerie Obenchain
- [BioC] merging VCF files
Valerie Obenchain
- [BioC] genome_intervals and GRange objects/HiTC package
Valerie Obenchain
- [BioC] genome_intervals and GRange objects/HiTC package
Valerie Obenchain
- [BioC] DataFrame bug?
Valerie Obenchain
- [BioC] Extracting strand information from GenomicFeatures transcript db objects
Valerie Obenchain
- [BioC] find gene symbols immediately flanking before and after a SNP position
Valerie Obenchain
- [BioC] curious behavior from VariantAnnotation 1.5.36
Valerie Obenchain
- [BioC] GENEID is missing when LOCATION is non-intergenic in VariantAnnotation package
Valerie Obenchain
- [BioC] GENEID is missing when LOCATION is non-intergenic in VariantAnnotation package
Valerie Obenchain
- [BioC] ExpressionSet Object
Valerie Obenchain
- [BioC] SNPassoc package data upload
Valerie Obenchain
- [BioC] merging VCF files
Valerie Obenchain
- [BioC] flip strand of GappedAlignmentPairs Object
Valerie Obenchain
- [BioC] flip strand of GappedAlignmentPairs Object
Valerie Obenchain
- [BioC] ties & strandedness in distanceToNearest GRanges
Valerie Obenchain
- [BioC] flip strand of GappedAlignmentPairs Object
Valerie Obenchain
- [BioC] normalize data in raster file
Erick Okuto
- [BioC] Problems with medianFilter in EBImage 4.0.0
Andrzej Oleś
- [BioC] R crashes when using CDF package generated using makecdfenv
Lars Rønn Olsen
- [BioC] quick question about rCytoscape
Ou, Jianhong
- [BioC] illegal operand when I run DEXSeq
Ou, Jianhong
- [BioC] illegal operand when I run DEXSeq
Ou, Jianhong
- [BioC] problem with pd.huex.1.0.st.v2 and oligo::getProbeInfo
Mikhail Pachkov
- [BioC] problem with pd.huex.1.0.st.v2 and oligo::getProbeInfo
Mikhail Pachkov
- [BioC] suppressing reduce() function when applying set operations to GRanges
Hervé Pagès
- [BioC] CharacerToFASTArecords
Hervé Pagès
- [BioC] adding papaya genome to BSgenome
Hervé Pagès
- [BioC] Extract Exon Features from GenomicFeatures Leads to Inconsistent Pairing of Gene and Exon IDs
Hervé Pagès
- [BioC] CharacerToFASTArecords
Hervé Pagès
- [BioC] speed of runmed on SimpleRleList
Hervé Pagès
- [BioC] speed of runmed on SimpleRleList
Hervé Pagès
- [BioC] Biostrings
Hervé Pagès
- [BioC] question about how to get ranges in Biostrings
Hervé Pagès
- [BioC] subset GRanges object via ElementMetadata
Hervé Pagès
- [BioC] subset GRanges object via ElementMetadata
Hervé Pagès
- [BioC] flip strand of GappedAlignmentPairs Object
Hervé Pagès
- [BioC] Bioinformatics Scientist
Agnès Paquet
- [BioC] EBImage: putting two images next to each others
Gregoire Pau
- [BioC] replicating ReadqPCR
James Perkins
- [BioC] Rotate xtick or ytick labels to any angle
Alexander Ploner
- [BioC] Accessing Bioconductor from Java
SHARANYA RAGHUNATH
- [BioC] package LIMMA design matrix for my experiment
RLW
- [BioC] LIMMA design matrix for my experiment
RLW
- [BioC] edgeR problem
Nima Rafati
- [BioC] edgeR problem
Nima Rafati
- [BioC] find gene symbols immediately flanking before and after a SNP position
Adaikalavan Ramasamy
- [BioC] find gene symbols immediately flanking before and after a SNP position
Adaikalavan Ramasamy
- [BioC] GENEID is missing when LOCATION is non-intergenic in VariantAnnotation package
Adaikalavan Ramasamy
- [BioC] GENEID is missing when LOCATION is non-intergenic in VariantAnnotation package
Adaikalavan Ramasamy
- [BioC] GENEID is missing when LOCATION is non-intergenic in VariantAnnotation package
Adaikalavan Ramasamy
- [BioC] Finding closest gene to chromosomal position (non-human or mouse)
Adaikalavan Ramasamy
- [BioC] normalized and Shift to 75.0 percentile
Paz Tapia Ramirez
- [BioC] IICAI-13 Call for papers
Venkateswara Rao
- [BioC] writeFastq writing dashes instead of dots
Thomas Rensch
- [BioC] writeFastq writing dashes instead of dots
Thomas Rensch
- [BioC] How to pool subgroups for makeContrasts() and subsequent limma analysis?
René
- [BioC] How to pool subgroups for makeContrasts() and subsequent limma analysis?
René
- [BioC] How to pool subgroups for makeContrasts() and subsequent limma analysis?
René
- [BioC] How to pool subgroups for makeContrasts() and subsequent limma analysis?
René
- [BioC] Detecting differential usage of introns from RNA-seq data.
Alejandro Reyes
- [BioC] Detecting differential usage of introns from RNA-seq data.
Alejandro Reyes
- [BioC] Detecting differential usage of introns from RNA-seq data.
Alejandro Reyes
- [BioC] Detecting differential usage of introns from RNA-seq data.
Alejandro Reyes
- [BioC] DEXSeq dexseq_prepare_annotation.py error
Alejandro Reyes
- [BioC] aggregate genes in DEXSeq
Alejandro Reyes
- [BioC] .pair to xys files
Markus Rienth
- [BioC] TMM Normalization without replicate
Mark Robinson
- [BioC] edgeR: counts or pseudo.counts?
Mark Robinson
- [BioC] Normalization
Vittoria Roncalli
- [BioC] Normalization
Vittoria Roncalli
- [BioC] R and High performance computing - Functions for Bioconductor users with large datasets
SPRINT
- [BioC] genoset:::initGenoSet
Schalkwyk, Leonard
- [BioC] genoset:::initGenoSet
Schalkwyk, Leonard
- [BioC] Conversion of minfi format MethylSet to methyAnalysis format MethyGenoSet
Ed Schwalbe
- [BioC] plotting BED intervals to TSS regions
Seb
- [BioC] plotting BED intervals to TSS regions
Seb
- [BioC] transform Illumina intensity for heatmap
Seb
- [BioC] transform Illumina intensity for heatmap
Seb
- [BioC] genome_intervals and GRange objects/HiTC package
Nicolas Servant
- [BioC] query on variance parameters for RMA
Hugh Shanahan
- [BioC] bug in graph::edgeData()
Paul Shannon
- [BioC] Aligning short reads to a single gene
Wei Shi
- [BioC] statistical test for time course data
Gordon K Smyth
- [BioC] statistical test for time course data
Gordon K Smyth
- [BioC] What does this mean in Limma?
Gordon K Smyth
- [BioC] LogFC query in Limma
Gordon K Smyth
- [BioC] Log transformation and left censoring
Gordon K Smyth
- [BioC] Log transformation and left censoring
Gordon K Smyth
- [BioC] statistical test for time course data
Gordon K Smyth
- [BioC] limma-voom and y$E
Gordon K Smyth
- [BioC] statistical test for time course data
Gordon K Smyth
- [BioC] Agilent Mouse 8x60K array
Gordon K Smyth
- [BioC] Filtering out tags with low counts in edgeR results in fewer differentially expressed genes.....
Gordon K Smyth
- [BioC] using offsets from EDASeq and cqn for edgeR
Gordon K Smyth
- [BioC] edgeR choose the best model of GLM
Gordon K Smyth
- [BioC] Design question: How to account for dependent samples?
Gordon K Smyth
- [BioC] AgiMicroRna for new Agilent Chip format
Gordon K Smyth
- [BioC] edgeR problem
Hayssam Soueidan
- [BioC] edgeR problem
Hayssam Soueidan
- [BioC] edgeR cpm filtering
John Sperry
- [BioC] edgeR cpm filtering
John Sperry
- [BioC] Question on Analyzing Illumina 450k methylation data
Srinivas Srikanth
- [BioC] Question on Analyzing Illumina 450k methylation data
Srinivas Srikanth
- [BioC] a diffBind problem
Rory Stark
- [BioC] DiffBind error loading dba.count
Rory Stark
- [BioC] Question concerning Diffbind
Rory Stark
- [BioC] a diffBind problem
Rory Stark
- [BioC] DiffBind - Scores for peakset are all the same
Rory Stark
- [BioC] DiffBind - Scores for peakset are all the same
Rory Stark
- [BioC] rhd5 reading variable-length strings
Steven
- [BioC] LogFC query in Limma
Roopa Subbaiaih
- [BioC] LogFC query in Limma
Roopa Subbaiaih
- [BioC] Error Bars on EdgeR
Ian Sudbery
- [BioC] PhD student in Quantitative Genetic Models of Complex Traits
Peter Sørensen
- [BioC] question about Gviz
Bogdan Tanasa
- [BioC] question about Gviz
Bogdan Tanasa
- [BioC] question about Gviz
Bogdan Tanasa
- [BioC] question about Gviz
Bogdan Tanasa
- [BioC] Problem of Ctrl+L in RStudio:
BH Tang
- [BioC] changes in SPIA package: using updated KEGG pathway data
Tarca, Adi
- [BioC] SPIA algorithm organisms not included already in the SPIA package
Tarca, Adi
- [BioC] flip strand of GappedAlignmentPairs Object
Stefanie Tauber
- [BioC] flip strand of GappedAlignmentPairs Object
Stefanie Tauber
- [BioC] flip strand of GappedAlignmentPairs Object
Stefanie Tauber
- [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
Taylor, Sean D
- [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
Taylor, Sean D
- [BioC] useDevel() not working
Dan Tenenbaum
- [BioC] using suitable R version for Bioconductor
Dan Tenenbaum
- [BioC] [devteam-bioc] Rsamtools installation error
Dan Tenenbaum
- [BioC] [devteam-bioc] Unable to
Dan Tenenbaum
- [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
Dan Tenenbaum
- [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
Dan Tenenbaum
- [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
Dan Tenenbaum
- [BioC] What happened to GenomicFeatures::spliceGraph?
Ryan Thompson
- [BioC] Finding genes with minimal expression across a set of conditions?
Ryan C. Thompson
- [BioC] package LIMMA design matrix for my experiment
Ryan C. Thompson
- [BioC] What happened to GenomicFeatures::spliceGraph?
Ryan C. Thompson
- [BioC] What happened to GenomicFeatures::spliceGraph?
Ryan C. Thompson
- [BioC] Normalization
Ryan C. Thompson
- [BioC] Normalization
Ryan C. Thompson
- [BioC] Normalization
Ryan C. Thompson
- [BioC] Normalization
Ryan C. Thompson
- [BioC] Normalization
Ryan C. Thompson
- [BioC] annotationTools: character vector clean-up
Ryan C. Thompson
- [BioC] annotationTools: character vector clean-up
Ryan C. Thompson
- [BioC] Bioconductor Digest, Vol 120, Issue 12
Thornton, Matthew
- [BioC] Bioconductor Digest, Vol 120, Issue 12
Thornton, Matthew
- [BioC] How to annotate Illumina HumanHT-12 v 3 expression beadchip?
Feng Tian
- [BioC] gmapR/gsnap crashes
Tim Triche, Jr.
- [BioC] rtracklayer weirdness
Tim Triche, Jr.
- [BioC] Required Annotation Package for Agilent-021974
Tim Triche, Jr.
- [BioC] gmapR/gsnap crashes
Tim Triche, Jr.
- [BioC] VariantAnnotation package with snp location
Tim Triche, Jr.
- [BioC] VariantAnnotation package with snp location
Tim Triche, Jr.
- [BioC] question about Gviz
Tim Triche, Jr.
- [BioC] question about Gviz
Tim Triche, Jr.
- [BioC] (missing?) UCSCKG -> SYMBOL mappings in Homo.sapiens (etc.)
Tim Triche, Jr.
- [BioC] curious behavior from VariantAnnotation 1.5.36
Tim Triche, Jr.
- [BioC] curious behavior from VariantAnnotation 1.5.36
Tim Triche, Jr.
- [BioC] A properly reproducible example of bizarre VariantAnnotation behavior
Tim Triche, Jr.
- [BioC] curious behavior from VariantAnnotation 1.5.36
Tim Triche, Jr.
- [BioC] Problem of Ctrl+L in RStudio:
Tim Triche, Jr.
- [BioC] Generate a GRangesList from a classical list of GRangesObjects
Tim Triche, Jr.
- [BioC] What happened to GenomicFeatures::spliceGraph?
Tim Triche, Jr.
- [BioC] What happened to GenomicFeatures::spliceGraph?
Tim Triche, Jr.
- [BioC] subset GRanges object via ElementMetadata
Tim Triche, Jr.
- [BioC] subset GRanges object via ElementMetadata
Tim Triche, Jr.
- [BioC] Finding closest gene to chromosomal position (non-human or mouse)
Tim Triche, Jr.
- [BioC] Package DRC: multiple treatment groups
Tim Triche, Jr.
- [BioC] Bumphunter and minfi
Tim Triche, Jr.
- [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
Tim Triche, Jr.
- [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
Tim Triche, Jr.
- [BioC] Differences in results analyzing Mouse Gene 1.0-ST using oligo and affy package
Jon Toledo
- [BioC] Differences in results analyzing Mouse Gene 1.0-ST using oligo and affy package
Jon Toledo
- [BioC] VariantAnnotation package with snp location
Fabrice Tourre
- [BioC] VariantAnnotation package with snp location
Fabrice Tourre
- [BioC] Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Stephen Turner
- [BioC] Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Stephen Turner
- [BioC] where is exonsOnTP53Genome defined
Wang, Sean
- [BioC] SNPassoc package data upload
Magdalena Wozniak
- [BioC] plotting BED intervals to TSS regions
Tengfei Yin
- [BioC] Visualization of alignments with mismatch bases
Tengfei Yin
- [BioC] Visualization of alignments with mismatch bases
Tengfei Yin
- [BioC] speed of runmed on SimpleRleList
Janet Young
- [BioC] speed of runmed on SimpleRleList
Janet Young
- [BioC] rGADEM: e-Values for reported motifs
Alexandra Zerck
- [BioC] Finding closest gene to chromosomal position (non-human or mouse)
Zhu, Lihua (Julie)
- [BioC] ChIPpeakAnno "examplePattern.fa" file
Zhu, Lihua (Julie)
- [BioC] ChIPpeakAnno "examplePattern.fa" file
Zhu, Lihua (Julie)
- [BioC] Pre-processing and probe removal in lumi
Matthias Zilbauer
- [BioC] Unable to
Alex [guest]
- [BioC] CHARM: Affymetrix 1.0R tiling arrays import
Andrew Beggs [guest]
- [BioC] structure of cfx file for HTqPCR
Brian Gorsuch [guest]
- [BioC] GSVA error
Chuanbao [guest]
- [BioC] AgiMicroRna for new Agilent Chip format - columns gTotalGeneSignal and gTotalProbeSignal missing
Constanze [guest]
- [BioC] using suitable R version for Bioconductor
Dr.Vijayakumar [guest]
- [BioC] edgeR import error
ES [guest]
- [BioC] XPS: Arabidopsis Gene 1.0 ST Array, import.exon.scheme ERROR
Endo [guest]
- [BioC] XPS: Arabidopsis Gene 1.0 ST Array, import.exon.scheme ERROR
Endo [guest]
- [BioC] HTqPCR
Franklin Johnson [guest]
- [BioC] HTqPCR: qPCRset
Franklin Johnson [guest]
- [BioC] reading in data in ReadqPCR
Franklin Johnson [guest]
- [BioC] replicating ReadqPCR
Franklin Johnson [guest]
- [BioC] reading in data in ReadqPCR
Franklin Johnson [guest]
- [BioC] workflow from NormqPCR 5.1 to 5.3
Franklin Johnson [guest]
- [BioC] Retrieving dN, dS from biomaRt fails: Attributes from multiple pages not allowed
Gabriel Teku [guest]
- [BioC] TMM Normalization without replicate
Jieon Lee [guest]
- [BioC] edgeR cpm filtering
John [guest]
- [BioC] DESeq Design issue
Joshua Pollack [guest]
- [BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Kaj Chokeshaiusaha [guest]
- [BioC] How to make a db package for Agilent-015354 Bovine Oligo Microarray (4x44K)?
Kaj Chokeshaiusaha [guest]
- [BioC] Error in sqliteExecStatement(con, statement, bind.data)
Kaj Chokeshaiusaha [guest]
- [BioC] R crashes when using CDF package generated using makecdfenv
Lars Rønn Olsen [guest]
- [BioC] problem with GDS2eSet function in GEOquery package
Laurent Pays [guest]
- [BioC] Extract microarray data for genes identified by GO analysis
Mark [guest]
- [BioC] CharacerToFASTArecords
Murli [guest]
- [BioC] Problem with sva() probably stemming from model.matrix()
Niles Oien [guest]
- [BioC] GO to Enzyme Commission number conversion!
Priya [guest]
- [BioC] Rotate xtick or ytick labels to any angle
Richard Hu [guest]
- [BioC] adding papaya genome to BSgenome
Rishi [guest]
- [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
Sean [guest]
- [BioC] where is exonsOnTP53Genome defined
Sean Wang [guest]
- [BioC] Simple question about Vector
Thiago [guest]
- [BioC] vegan, accumulation curve
Utpal Bakshi [guest]
- [BioC] Differential Expression analysis
abdul rawoof [guest]
- [BioC] Differential Expression analysis
abdul rawoof [guest]
- [BioC] DEXSeq dexseq_prepare_annotation.py error
minyoung [guest]
- [BioC] Rsamtools installation error
tkhodges [guest]
- [BioC] query regarding erroers
urvesh patel [guest]
- [BioC] query regarding memory allocation...please help
urvesh patel [guest]
- [BioC] runSPIA() in graphite package
array chip
- [BioC] runSPIA() in graphite package
array chip
- [BioC] 回复:Re: GSVA error
chuanbao
- [BioC] Question: GSVA error
chuanbao
- [BioC] Biorad iCycler cfx manager files and HTqPCR
b1gorsuch at comcast.net
- [BioC] edgeR GLM : family based experimental design
gianfilippo coppola
- [BioC] XPS: Arabidopsis Gene 1.0 ST Array, import.exon.scheme ERROR
cstrato
- [BioC] XPS: Arabidopsis Gene 1.0 ST Array, import.exon.scheme ERROR
cstrato
- [BioC] XPS: Arabidopsis Gene 1.0 ST Array, import.exon.scheme ERROR
cstrato
- [BioC] ComBat: How to choose multiple covariates in ComBat analysis- Need advice
hu duan
- [BioC] ComBat: How to choose multiple covariates in ComBat analysis- Need advice
hu duan
- [BioC] (no subject)
capricy gao
- [BioC] A Ph.D. Student’s CRY for Help
saidi34 at hushmail.com
- [BioC] [Course] CSAMA 2013: Computational Statistics for Genome Biology (11th edition) Brixen, Italy, June 24-28th 2013
stefano iacus
- [BioC] Bumphunter output
khadeeja ismail
- [BioC] Bumphunter output
khadeeja ismail
- [BioC] John linux-user
John linux-user
- [BioC] Regarding Limma differential expression.
nitin mandloi
- [BioC] counting BAM reads in a set of genomic regions
mattia pelizzola
- [BioC] Introductory workshop for RNA-seq 27-28 March 2013, Torino, Italy
rcaloger
- [BioC] Creating annotation database for GOstat
naomi at stat.psu.edu
- [BioC] qvalue pi0 computation
naomi at stat.psu.edu
- [BioC] transcriptDb object not found when call locateVariants() in a function
sun
- [BioC] transcriptDb object not found when call locateVariants() in a function
sun
- [BioC] Problem installing packages on new R
v.leoncikas at surrey.ac.uk
- [BioC] Issues while installing RBGL package
jason tyler
- [BioC] AUTO: Pie Müller is out of the office. (returning 18.02.2013)
Pie.Mueller at unibas.ch
- [BioC] R and High performance computing - Functions for Bioconductor users with large datasets
shirley zhang
Last message date:
Thu Feb 28 23:51:58 CET 2013
Archived on: Fri Mar 1 07:54:36 CET 2013
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