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2
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Problems with summarizeOverlaps
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updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 10
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Reading Large File in Trunk
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updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 110
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DESeq2 output with multiple Ensembl Gene Names per row, how to resolve?
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updated 8.6 years ago by 43k • written 8.6 years ago by • 0
1
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1
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1.2k
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Obtain exactly the interval that overlap
findoverlaps Granges
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ▴ 30
0
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0
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problem using ensemblVEP with GRC37
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8.6 years ago mikko.arvas • 0
1
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1
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Window size for MEDIPS
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updated 8.6 years ago by ▴ 570 • written 8.6 years ago by • 0
2
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topGO gene names/ensembl IDs
topgo biomart deseq2 gene ontology
updated 8.6 years ago by ▴ 760 • written 8.6 years ago by ▴ 10
1
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1
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TFBSTools: Appending objects to PFMatrixList
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8.6 years ago nathan.lawlor03 • 0
0
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sangerseqR::read.abif reads float data incorrectly on little-endian systems
sangerseqR bug
8.6 years ago brendan.furneaux ▴ 10
0
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0
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Job: Hunting for Human Infectious Agents in Cancer using data from Genomics England's 100,000 genome project : PhD Studentship @ UEA, Norwich
phd cancer pathogens NGS Job
8.6 years ago Daniel Brewer ▴ 100
1
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0
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Job: Biomarker Data Analysis: Development of a Test for Prostate Cancer : PhD Studentship @ UEA, Norwich
phd cancer Job
8.6 years ago Daniel Brewer ▴ 100
0
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4
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beadarray: readIllumina with sample sheet broken due to Illumina switching to 12 digit chip identifiers
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updated 8.6 years ago by ★ 1.1k • written 8.7 years ago by • 0
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Multiple comparisons for DE analysis with DESeq2
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updated 8.6 years ago by ▴ 690 • written 8.6 years ago by ▴ 10
0
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1
reply
793
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Contrast matrix with 2 columns
limma microarray
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
0
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2
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MeQA and MEDIPS
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updated 8.6 years ago by • 0 • written 9.6 years ago by • 0
2
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3
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Split Genomic Ranges With Reference Overlaps (Centromere)
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written 8.6 years ago by • 0
0
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3
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Handling outliers in DESeq2?
deseq2 sample outliers
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
2
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2
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2.7k
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SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva removebatcheffect R
updated 8.6 years ago by ▴ 130 • written 8.7 years ago by ▴ 10
0
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1
reply
1.7k
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how to extract complex contrast with DESeq2
contrast DESeq2 differential gene expression
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 90
1
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5
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3.5k
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Error with read.idat() function in illuminaio package
illuminaio normalization
updated 8.6 years ago by ▴ 1000 • written 10.4 years ago by ▴ 600
2
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2
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1.5k
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Findoverlaps insame sample
genomicranges granges findoverlaps
8.6 years ago julrodr80 ▴ 30
4
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4
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3.3k
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Using duplicateCorrelation to handle replicate samples
limma duplicatecorrelation replicates
8.7 years ago • updated 8.6 years ago rwalke13 • 0
3
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9
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12k
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Does GSVA enrichment score comes negative?
GSVA
9.5 years ago • updated 8.6 years ago pbachali ▴ 50
2
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1
reply
1.7k
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GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 90
0
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924
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MetaboSignal won't work due "Image not found"
MetaboSignal
8.6 years ago sandra.therrien.laperriere • 0
0
votes
1
reply
1.8k
views
derfinder fullCoverage() changes chromosome style and then regionMatrix() complains and ignores provided 'currentStyle'
derfinder
8.6 years ago Wayne • 0
0
votes
7
replies
3.0k
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regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder GenomeInfoDb GenomicRanges
8.7 years ago • updated 8.6 years ago Wayne • 0
0
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1
reply
2.5k
views
Gviz: AnnotationTrack - text (feature id) annotation overlay
gviz
updated 8.6 years ago by • 0 • written 10.6 years ago by • 0
0
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4
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deseq2 with one treated sample and one control sample of RNA-seq readcounts
deseq2
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
0
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0
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News: ensembl 87 and 88 gtfs and fasta twobits have been added to AnnotationHub
bioconductor annotationhub News
8.7 years ago shepherl 4.2k
0
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0
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951
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DEXSeq : for differential exon usage
DEXSeq R
8.7 years ago gv ▴ 40
0
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2
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1.5k
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loading vcf with readVcf
bioconductor
updated 8.7 years ago by 68k • written 8.7 years ago by ▴ 110
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lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi illumina normalization beadarray
8.7 years ago hkarakurt ▴ 20
0
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5
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4.8k
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GC content and length bias correction with DESeq2 using cqn normalization factor matrix
deseq2 cqn noiseq
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 10
0
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1
reply
1.7k
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FUNCTIONAL ENRICHMENT ANALYSIS
genecodis3 fdr
updated 8.7 years ago by ★ 3.4k • written 8.7 years ago by ▴ 30
10
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1
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3.1k
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How to explain how DESeq2 works to someone with zero bioinformatics background?
deseq2
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
0
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0
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OmicCircos: included UCSC.hg19.chr dataframe is actually hg18 cytobands
omiccircos bug hg19 hg18 data
8.7 years ago matthew.bashton • 0
8
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3
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GSVA indifferent to 'abs.ranking'
GSVA gsva abs.ranking
updated 8.7 years ago by ★ 3.4k • written 8.7 years ago by ▴ 130
0
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1
reply
1.4k
views
How to solve out the misunstanding of fake "red" "green" on the heatmap
pheatmap
updated 8.7 years ago by ▴ 690 • written 8.7 years ago by ▴ 50
0
votes
2
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2.0k
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should i include PCs or MDSs as covariates in methylation study?
limma methylation R covariate MDS
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
2
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5
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4.0k
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deseq2 multifactor timeseries help
deseq2 multifactorial design time course
updated 8.7 years ago by • 0 • written 8.7 years ago by ▴ 10
0
votes
2
replies
946
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BiomaRt xenopus tropicalis genome unavailable
bioconductor biomart xenopus xenbase
updated 8.7 years ago by ★ 6.6k • written 8.7 years ago by • 0
0
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11
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Unable to load package 'hgu95acdf' after upgrading to R 3.4.0
hgu95acdf
8.7 years ago sue.wilson • 0
1
vote
2
replies
1.7k
views
BiocCheck path escape issue
bioccheck bug
8.7 years ago Michael Steinbaugh ▴ 90
0
votes
0
replies
843
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rpubchem is not working , or is it ?
rpubchem
8.7 years ago bioinformatics ▴ 30
0
votes
0
replies
891
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Parallel version of viewApply?
viewApply biocparallel
8.7 years ago maltethodberg ▴ 180
0
votes
11
replies
2.8k
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DiffBind: failed to run dba.count in SSH
SSH atac-seq
updated 8.7 years ago by ▴ 670 • written 8.7 years ago by • 0
0
votes
1
reply
1.7k
views
ConsensusClusterPlus - function "calcICL" - How the samples are ordered in the plots???
ConsensusClusterPlus calcICL plot
9.1 years ago • updated 8.7 years ago juan-pablo.cerapio-arroyo ▴ 10
0
votes
2
replies
1.2k
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Running DEXSeq in a distributed setting
DEXSeq LSF Distributed Computing
8.7 years ago vakul.mohanty ▴ 20
1
vote
2
replies
1.8k
views
rowRanges in Summarized Experiment changes counts
deseq2 summarizedexperiment rangedsummarizedexperiment rnaseq
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 10
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