October 2013 Archives by thread
Starting: Tue Oct 1 02:00:16 CEST 2013
Ending: Thu Oct 31 23:37:56 CET 2013
Messages: 554
- [BioC] GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Luo Weijun
- [BioC] Job: Bioinformatician in Livestock Virology
Jan Kim
- [BioC] fdr cutoff
Richard Friedman
- [BioC] CANCELED: Boston Bioconductor Basics, Oct 10-11 2013
Vincent Carey
- [BioC] Regarding miRNA analysis
deepika lakhwani
- [BioC] need additional sanity checks in TabixFile or readVcf
Jeremy Leipzig
- [BioC] VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'
Valerie Obenchain
- [BioC] limma: paired + multiple comparisons + technical replication ?
Sarah Bonnin
- [BioC] pathview
Hilary Smith
- [BioC] Saving all AffyPLM residual plots to disk
Peterson, Leif
- [BioC] Creat PWM from Alignment with Gaps
Hervé Pagès
- [BioC] Finding Candidate Binding Sites for multiple Known Transcription Factors simultaneously
Hervé Pagès
- [BioC] Genentech Biostat Summer Intern Program 2014
Maoxia Zheng
- [BioC] summarizeOverlaps behavior on RNA-Seq paired end stranded data
Abhishek Pratap
- [BioC] Fwd: summarizeOverlaps behavior on RNA-Seq paired end stranded data
Abhishek Pratap
- [BioC] Problem in reading SNP hapmap data
Xiaolian Yuan
- [BioC] Measuring shifts in intronic expression independently of exons
James Perkins
- [BioC] using a connection with makeTranscriptDbFromGFF()
Blanchette, Marco
- [BioC] Bioconductor refLocs2TranscriptLocs function
Michael Lawrence
- [BioC] [devteam-bioc] Why does a GOAllFrame contain more rows than its argument GoFrame?
Marc Carlson
- [BioC] Genbank accession annotation?
Ed Siefker
- [BioC] Negative Width error in cn.mops
Susan VanderPlas
- [BioC] targetscan PCT score of NULL
yotsawat pomyen [guest]
- [BioC] display of chromosome-chromosome interactions
Bogdan Tanasa
- [BioC] Subject= using beadarray to process iscan expression data - error using readIllumina()
Alan L Hutchison
- [BioC] Formatting in R
Ovokeraye Achinike-Oduaran
- [BioC] ka
Kaj Chokeshaiusaha [guest]
- [BioC] Creating Annotation package for GPL10427
Kaj Chokeshaiusaha [guest]
- [BioC] custom variant AnnotationDbi?
Francesco Lescai
- [BioC] Comparing microarray data from different platforms
Ahmet Sinan Yavuz
- [BioC] Protein domain identification using bioconductor packages
Delasa Aghamirzaie
- [BioC] Overlapping region: Segment 0 error with processSwathData() for HumanHT12v4 microarray bead data
Alan Hutchison
- [BioC] snpStats/GWASTools conversion
Stephanie M. Gogarten
- [BioC] ensemblVEP, variant_effect_predictor versions and release schedule
Thomas Sandmann [guest]
- [BioC] GAGE and PATHVIEW packages
Christian De Santis
- [BioC] locate a target species in Refseq ftp directory
heyi xiao
- [BioC] Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions
Nitesh Turaga
- [BioC] Mapping Affymetrix annotations with Bioconductor annotations
Joao Sollari Lopes
- [BioC] looking for data file for ATH1 (GPL198)
Matthew McCall
- [BioC] R 3.0.0 problems installing flowCore and other packages
Sisi Chen [guest]
- [BioC] Error in installing Gviz
马磊
- [BioC] DEXSeq: Paired End Analysis
Margaret Linan
- [BioC] GRangesList mcols names
Leonard Goldstein
- [BioC] DEXSeq Paired-end analysis (new issues)
Margaret Linan
- [BioC] DEXSeq update
Margaret Linan
- [BioC] overlay in GVIZ
Hahne, Florian
- [BioC] limma package, using a covariate?
Alasaari Jukka
- [BioC] Summarized Experiments - Combine
Garcia Manteiga Jose Manuel
- [BioC] IdeogramTrack and bigWig file errors in Gviz
Miles Pufall
- [BioC] ShortReadQ constructor
Ivan Gregoretti
- [BioC] multicore version of maanova
Ric Hux [guest]
- [BioC] Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions
Zhang, Jitao David
- [BioC] help with forging a BSgenome data
Hervé Pagès
- [BioC] Getting GO ids for genenames in plasmodium falciparum
Ipsi [guest]
- [BioC] arrayQualityMetrics does not produce interactive plots
Steven Cowman [guest]
- [BioC] Advice to RIPSeeker users to improve RAM and CPU use
Davis, Wade
- [BioC] advice on masked objects
Bogdan Tanasa
- [BioC] variation between chips - neqc()
Rao,Xiayu
- [BioC] egdeR troubles under new R 3.02
alogmail2 at aol.com
- [BioC] MEDIPS
Paolo Kunderfranco
- [BioC] [maSigPro] two color array analysis of time series in different cell lines.???
Neeraj Rana
- [BioC] hgug4845a.db - error in the lookUp function when running genes.rpt.agi
Pitea Adriana
- [BioC] limma_3.17.23 - missing ILMN identifiers in EList objects after read.ilmn
Kemal Akat
- [BioC] ChIPpeakAnno Question, regarding BED scores
Zhu, Lihua (Julie)
- [BioC] Question about PCA and transformed data in DESeq2
amandine.fournier at chu-lyon.fr
- [BioC] HTqPCR normalization issues - third posting
Alessandro Guffanti [guest]
- [BioC] creating a newCountDataSet from HTSeq-count
Assa Yeroslaviz
- [BioC] Normalization before ComBat
Johnson, William Evan
- [BioC] Pathview graph with multiple states/samples or time series
Luo Weijun
- [BioC] EDASeq within normalization
Catarina Almeida
- [BioC] maSigPro dataset information
Paola [guest]
- [BioC] Lumi failed to load
Hitoshi Okada
- [BioC] Install DESeq2 on windows R 3.0.1/2
刘鹏飞
- [BioC] GenomicFeatures loadDb error
Linxzh [guest]
- [BioC] Questions about DESeq2 (new version and filtering low counts)
amandine.fournier at chu-lyon.fr
- [BioC] Error in estimateCommonDisp
xiaowan.lu at uhnresearch.ca
- [BioC] mifi unable to install by bioLite
Hitoshi Okada
- [BioC] How does one deal with spatial effects detected on single channel microarrays?
Scott Robinson
- [BioC] multiple annotations with get()?
Ed Siefker
- [BioC] BiocGenerics::plotMA (was: "egdeR troubles under new R 3.02")
Wolfgang Huber
- [BioC] Setting weight to agilent source
Kaj Chokeshaiusaha [guest]
- [BioC] DNaseR - a new Bioconductor package for DNase-seq digital genomic footprinting
Pedro Madrigal
- [BioC] CexoR: new Bioconductor package for peak-pair calling in ChIP-exo data with replicates
Pedro Madrigal
- [BioC] how to install from file (whithout net access) ?
Jean-Christophe Penalva
- [BioC] select CPM value and what does logFC value mean_edgeR
Naresh Vasani
- [BioC] Rsamtools: readGAlignmentsFromBam weird behavior reading MAPQ and RNEXT fields
rubi [guest]
- [BioC] Course Announcement - Next Generation Data Analysis with R/Bioc (Dec 12-16, 2013)
Thomas Girke
- [BioC] Modify plot - genas function from LIMMA
Christian De Santis
- [BioC] Retreving mRNA subsequence (GenomicFeatures, BSgenome)
Lukasz [guest]
- [BioC] DESeq: help with analysis
Abhishek Pratap
- [BioC] Bioconductor 2.13 is released
Dan Tenenbaum
- [BioC] Comparing DNAStringSetLists
Vince S. Buffalo
- [BioC] VennDiagrams, decideTests and topTable
Christian De Santis
- [BioC] Installing Gostat
R [guest]
- [BioC] New release of triplex package
Jiří Hon
- [BioC] RNA differential expression
Liliane Santana
- [BioC] Excluding probes during methylation analysis
Victoria Svinti
- [BioC] error loading dba in DiffBind
Ankit Arora
- [BioC] Pathview and GAGE now work with essentially all KEGG species
Luo Weijun
- [BioC] Biobase - Error: ExpressionSet
Lisa Cohen
- [BioC] GenomicFeatures- disjointExons error
Zhu, Lihua (Julie)
- [BioC] Illumina spike-in probe sequences, lumi
Rohmatul Fajriyah
- [BioC] stranded intronic variants with VariantAnnotation::locateVariants()
Robert Castelo
- [BioC] Computing the coverage on a bamfile with a huge amount of seqlevels
Stefanie Tauber
- [BioC] Deseq: Difference in number of reads
Rushiraj Manchiganti
- [BioC] DiffBind Question
Rory Stark
- [BioC] arrayQualityMetrics - undefined columns selected
Lisa Cohen
- [BioC] Patient effect as fixed or random effect
bigoun
- [BioC] AffyPLM
M. van Duin
- [BioC] QuasR on Linux Cluster
Ugo Borello
- [BioC] Ensembl or Gencode version of TxDb.Hsapiens.UCSC.hg19.knownGene
Adaikalavan Ramasamy
- [BioC] Problems with DiffBind
Rory Stark
- [BioC] autoplot transcriptDb error with some regions
Alejandro Reyes
- [BioC] Paired data for DEseq2: Multifactorial design
Sindre Lee
- [BioC] pathview -- ID Problem?
fabian [guest]
- [BioC] BStringSet not work with lists of many DNAString elements
heyi xiao
- [BioC] error when running makeVectorsAffyBatch
Loraine, Ann
- [BioC] Getting first or last hit from a Hits object
Peter Hickey
- [BioC] Is there a package for peptide alignment with protein sequences?
Xiaoyun [guest]
- [BioC] Too many DEG with edgeR output?
Bernardo Bello
- [BioC] Whole genome amino acid composition package?
Bernardo Bello
- [BioC] RNAseq in silico simulator
Dave Gerrard
- [BioC] edgeR adding RefSeq IDs
Robin [guest]
- [BioC] deseq2 plotMA
Garcia Manteiga Jose Manuel
- [BioC] lower.limits and upper.limits in glmnet
Yue Li
- [BioC] A question when using Biostrings
Hervé Pagès
- [BioC] makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
刘鹏飞
- [BioC] analyses of CGH data
Isha Pandey Phd Scholar BITS Pilani Campus
- [BioC] how to obtain base counts from BAM file at specific genomic coordinates
Hervé Pagès
- [BioC] Question about rtracklayer GenomicRanges bed export order
Nathan Sheffield [guest]
- [BioC] Directed MST (Edmond's Algorithm)
Forst, Christian
- [BioC] edgeR with two different groups (unpaired) at two time points (paired): Need some input
Sindre Lee
- [BioC] how to filter downloading SRA data
Wang Peter
- [BioC] 450k annotation packages compatible version and analysis with blockFinder (minfi)
Florence Cavalli
- [BioC] Rsubread segfault
James W. MacDonald
- [BioC] Rsubread featureCounts question
James W. MacDonald
- [BioC] Coercing matrix into expression set, for normalization of only subsets of miRNAs (affy miRNA3.0)
Dana Most
- [BioC] minfi: RGChannelSet for illumina 27k data
Brian Smith
- [BioC] minfi: RGChannelSet
Brian [guest]
- [BioC] segfault ReadAffy cause 'memory not mapped'
Brian D. Peyser PhD
- [BioC] affy - Anotation of Afymetrix PrimeView chipe
Adam Olejnik
- [BioC] working with genome-wide phastCons scores
Robert Castelo
- [BioC] 'RmiR.Hs.miRNA' DB versions and filtering criteria?
Hamid Bolouri
- [BioC] makeVennDiagram
Zhu, Lihua (Julie)
- [BioC] Integration of different microarray data (same platform)
Chirag Gupta [guest]
- [BioC] edgeR: Treatment effect at any time (UG3.3.3)
Matt McNeill
- [BioC] enrichment packages that accept t-stat (or related stat) as input
Pekka Kohonen
- [BioC] Cannot upgrade bioconductor from 2.12 to 2.13
A M Torres, Hugo
- [BioC] Genome Browser and R
khadeeja ismail
- [BioC] error in reading files using HTqPCR
Aashiq Hussain Mirza
- [BioC] How to get length information for mm10 genome and geneID gene Symbol?
Thanh Hoang
- [BioC] paired samples and time course experiments in LIMMA
Lauren Sassoubre
- [BioC] readVcf fails when ALT field contains breakends and no symbolic allele
Daniel Cameron [guest]
- [BioC] MEDIPS rms normalization by input
Herve Acloque [guest]
- [BioC] Error in extracting genes from Goterms using GOStats package
Sandy
- [BioC] Extracting genes associated to GO terms
paul [guest]
- [BioC] Sequence Distance matrix with large sequences
Benjamin Ward (ENV)
- [BioC] DESeq2 new error coming up
Alicia R. Pérez-Porro
- [BioC] package installation bei Rdevel fails
Stefanie Tauber
- [BioC] [Fwd: package installation bei Rdevel fails]
Stefanie Tauber
- [BioC] ComBat: Working with no replicates
Pedro Furió Tarí
- [BioC] Installing library package (Marmoset Gene 1.0 ST Array) into R environment
DR DHANJIT KUMAR DAS [guest]
- [BioC] Reading a FASTA file in R
Subhajit [guest]
- [BioC] upload multiple genelists at a time for GO or pathway enrichment
Helen Smith
- [BioC] ComBat
Kovyrshina, Tatiana
- [BioC] oligo package reading in cel files
oligo user [guest]
- [BioC] rhdf5, dataframes, and variable length strings
John Estrada [guest]
- [BioC] New GO terms after TopGO enrichment?
Bernardo Bello
- [BioC] New GO terms after TopGO enrichment? (updated)
Bernardo Bello
- [BioC] dmrFinder error
genefan [guest]
- [BioC] the
Wang Peter
- [BioC] flowCore: troubles reading FCS files from Calibur
Anja Mirenska
- [BioC] About your motifStack package
Ou, Jianhong
- [BioC] FW: About your motifStack package
Ou, Jianhong
- [BioC] Problem with topTable function (after Bioconductor update)
Christian De Santis
- [BioC] European Developers' Meeting 2013
Jonathan Cairns
- [BioC] Working with ensembl 73 & BSGenome
Timothy Johnstone [guest]
- [BioC] setting names of GAlignmentsList objects
Hans-Ulrich Klein
- [BioC] Unable to load xps...
Bas Jansen
- [BioC] Problem with the oligo package for nimblegen analysis
isabelle goncalves [guest]
- [BioC] Patient and matched control paired data
Steve [guest]
- [BioC] combine the values from two column into one
Nikul Soni
- [BioC] MethyLumiM to MethyLumiSet?
Allegra Petti
- [BioC] getting RPKM or TPM values
Nikolay N.
- [BioC] Error in heatmapSig function
Maria Mengual [guest]
- [BioC] Create a sample file /tab delimited file in QuasR
chris [guest]
- [BioC] perspective on differential expression counting - unmapped reads?
Jon BR
- [BioC] help with limma design, contrast matrices
Lisa Cohen
Last message date:
Thu Oct 31 23:37:56 CET 2013
Archived on: Thu Oct 31 23:38:17 CET 2013
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