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Votes
0
votes
3
replies
6.7k
views
Biostrings character vector conversion
biostrings
9.7 years ago
ribioinfo
▴ 100
0
votes
2
replies
1.1k
views
Estimate dispersion DESeq2 and gene number
deseq2
9.7 years ago
ribioinfo
▴ 100
0
votes
0
replies
1.3k
views
Help in interpreting the plot of the function plotRLDF in limma package for microarray dataset concerning two categorical classes
limma
plotRLDF
microarray
classification
linear discriminant function
9.7 years ago
svlachavas
▴ 840
0
votes
0
replies
1.3k
views
Job:
Post-doctoral position in algorithms for cancer data analysis
algorithms
ChIP-seq
cancer
Job
9.7 years ago
valentina.boeva
• 0
6
votes
7
replies
2.8k
views
Requesting flank sequences (BioMart::Exception)
biomart
plants_mart
updated 4.9 years ago by
lessismore
▴ 20 • written 9.7 years ago by
pbarros
• 0
0
votes
1
reply
1.5k
views
Problem installing Bioc Workflows
rnaseq
workflows
bioconductor
9.7 years ago
Hadi Gharibi
• 0
4
votes
4
replies
2.9k
views
How to handle the change in resultsNames() for DESeq2 ?
deseq2
resultsnames
multifactorial design
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
Ira
▴ 10
1
vote
2
replies
1.2k
views
Thresholded testing in edgeR for only positive log fold changes
edger
updated 9.7 years ago by
Aaron Lun
★ 29k • written 9.7 years ago by
le2336
▴ 20
3
votes
5
replies
2.2k
views
DESeq2 multifactor and paired sample analysis
deseq2
9.7 years ago
amy
• 0
1
vote
0
replies
1.4k
views
Job:
Summer Studentship in Data Science (Cancer Research) at the University of Cambridge
cancer
summer studentship
Job
9.7 years ago
Shamith.Samarajiwa
▴ 180
2
votes
1
reply
1.4k
views
inconsistent results from applyPileups and pileLettersAt
Rsamtools
GAlignments
pileup
updated 9.7 years ago by
Martin Morgan
25k • written 9.7 years ago by
jesper.gadin
▴ 10
4
votes
9
replies
2.4k
views
limma paired design with continous covariate
limma
paired
covariate
updated 9.7 years ago by
Steve Lianoglou
★ 13k • written 9.7 years ago by
meeta.mistry
▴ 30
2
votes
1
reply
1.4k
views
Use matchPattern for large DNAStrings
biostrings
annotate
updated 9.7 years ago by
Hervé Pagès
16k • written 9.7 years ago by
Vinicius Henrique da Silva
▴ 40
4
votes
3
replies
5.5k
views
How to do a confounding variable adjustment without using the treatment information?
deseq2
rnaseq_analysis
variancestabilizingtransformation
confounders
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
ompandey
▴ 10
0
votes
5
replies
1.9k
views
Error Raised When Trying To Use pileup()
hilbertvis
rsamtools
shortread
biostrings
updated 9.7 years ago by
Martin Morgan
25k • written 9.7 years ago by
travis.m.couture
• 0
0
votes
2
replies
1.7k
views
permutation with plink
illumina
plink
permutation
updated 9.7 years ago by
James W. MacDonald
68k • written 9.7 years ago by
sedrinne
• 0
1
vote
2
replies
950
views
how/what to use to perform Differential Expression Gene if log2 available?
microarray
limma
edgeR
updated 9.7 years ago by
Gordon Smyth
53k • written 9.7 years ago by
Michael
• 0
0
votes
2
replies
1.7k
views
Broken AnnotationHub resource (AH21414 | grasp2)
annotationhub
grasp2
grasp2db
updated 9.7 years ago by
Valerie Obenchain
★ 6.8k • written 9.7 years ago by
Peter Hickey
▴ 760
3
votes
11
replies
3.4k
views
should I use rsem's summary to genes or tximport's?
tximport
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
ty.thomson
▴ 10
0
votes
0
replies
1.1k
views
I am getting a champ error during BatchNorm
ChAMP
illumina methylationepic 450k
9.7 years ago
brenna.hott
• 0
0
votes
1
reply
836
views
modified the header data in the fixed slots of a VCFHeader object
variantannotation
updated 9.7 years ago by
Michael Lawrence
★ 11k • written 9.7 years ago by
delphine.charif
• 0
2
votes
3
replies
1.1k
views
DEGs : finding DE genes specific for one condition
deseq2
R
rnaseq
9.7 years ago
alva.james
• 0
0
votes
0
replies
1.4k
views
ggbio plotIdeogram(..., zoom.region) broken ?
ggbio
biovizBase
9.7 years ago
kevin.rue
▴ 350
3
votes
5
replies
2.0k
views
Run DESeq with only a handful of genes
deseq2
Small number of genes
software error
9.7 years ago
xinlian.zhang25
• 0
0
votes
1
reply
1.4k
views
Questions about the correct implementation of the function plotRLDF from R package limma regarding classification of a microarray dataset
limma
microarray
plotRLDF
classification
9.7 years ago
svlachavas
▴ 840
1
vote
3
replies
2.4k
views
Bioc 3.3 Windows 10 eiR package fails to install
software error
R
cheminformatics
package installation
eiR
updated 9.7 years ago by
khoran
▴ 10 • written 9.7 years ago by
rjrich
• 0
4
votes
5
replies
1.8k
views
parRapply in BiocParallel ?
biocparallel
variantannotation
updated 9.7 years ago by
Michael Lawrence
★ 11k • written 9.7 years ago by
kevin.rue
▴ 350
3
votes
2
replies
2.4k
views
Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file
snprelate
GWASTools
updated 9.7 years ago by
Adrienne Stilp
▴ 30 • written 9.7 years ago by
Vinicius Henrique da Silva
▴ 40
1
vote
7
replies
1.9k
views
Biomart: listMarts, listFilters and listAttributes work, but getBM doesn't
biomart
updated 9.7 years ago by
James W. MacDonald
68k • written 9.7 years ago by
invlasov
• 0
0
votes
3
replies
3.2k
views
Annotation in ExpressionSet object
ExpressionSet
globaltest
9.7 years ago
NS
▴ 60
1
vote
3
replies
1.7k
views
VennDiagram from two TestResults matrices
limma
venn diagram
updated 9.7 years ago by
Gordon Smyth
53k • written 9.7 years ago by
shania90.lk
▴ 10
0
votes
0
replies
1.6k
views
plotting normalized RPM coverage for plus and minus strands in gviz
gviz
rsamtools
9.7 years ago
amias
▴ 10
1
vote
5
replies
2.4k
views
Error using Rsubread align: caugh segfault invalid permissions
rsubread
align
segfault
updated 9.7 years ago by
Wei Shi
★ 3.6k • written 9.7 years ago by
gerard_llimos
▴ 10
9
votes
6
replies
4.5k
views
about paired-samples in edgeR
edger
9.7 years ago
Bogdan
▴ 670
0
votes
1
reply
1.3k
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 9.7 years ago by
Aaron Lun
★ 29k • written 9.7 years ago by
wliao
• 0
1
vote
4
replies
2.6k
views
DESeq2 "results" Error in .classEnv(classDef)
deseq2
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
p2016k
• 0
2
votes
25
replies
8.6k
views
How to use Limma to analyze differences among group items without doing pairwise comparisons
limma
9.8 years ago • updated 9.7 years ago
sami.pietila
• 0
2
votes
6
replies
3.9k
views
Clustering and bootstrapping of RNASeq samples
clustering
pvclust
vsd
edgeR
rnaseq
written 9.7 years ago by
Jane Merlevede
▴ 90
0
votes
0
replies
2.0k
views
methyAnalysis error with example data
methyanalysis
9.7 years ago
Tom
▴ 10
1
vote
4
replies
1.8k
views
Error using countBam (Rsamtools package)
rsamtools
countbam
9.7 years ago
t.kuilman
▴ 170
0
votes
0
replies
1.0k
views
How to calculate risk of relapse based on subtypes and proliferation (ROR-P) PAM50 sub-typing?
RORP
PAM50
9.7 years ago
g_draculla
▴ 10
0
votes
3
replies
2.1k
views
Trouble with Custom PC Plot
deseq2
plotPCA
PCA
rna-seq
9.7 years ago
newsomew13
• 0
0
votes
1
reply
958
views
question for SVA package
getting error in gsva function
updated 9.7 years ago by
Jeff Leek
▴ 650 • written 9.7 years ago by
js2182
• 0
5
votes
4
replies
2.1k
views
Is there a way to remove or take the first overlapping gene(s) when using makeTxDbFromGFF?
genomicfeatures
updated 9.7 years ago by
Hervé Pagès
16k • written 9.7 years ago by
endrebak85
▴ 40
1
vote
1
reply
2.5k
views
Null model in SVA for patient paired test comparing tumor vs normal
sva
paired samples
rnaseq
updated 9.7 years ago by
Jeff Leek
▴ 650 • written 9.7 years ago by
gumilton
• 0
0
votes
6
replies
3.1k
views
EBImage readImage hangs when reading tif file with multiple frames.
software error
ebimage
updated 9.7 years ago by
Andrzej Oleś
▴ 750 • written 9.7 years ago by
krassk
• 0
0
votes
1
reply
1.2k
views
[VariantAnnotation] Unable to set a genotype with geno()
variantannotation
updated 9.7 years ago by
shepherl
4.3k • written 9.7 years ago by
delphine.charif
• 0
1
vote
6
replies
1.9k
views
Are these contrasts correct for use in DESeq2?
deseq2
contrast
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
Jane Merlevede
▴ 90
6
votes
4
replies
2.2k
views
Clarification on DESeq2 normalizationFactors(), estimateDispersions() and varianceStabilizingTransformation()
deseq2
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
enricoferrero
▴ 680
5
votes
7
replies
2.6k
views
Gviz: How to plot UTRs with GRanges object?
gviz
updated 9.7 years ago by
florian.hahne@novartis.com
★ 1.6k • written 9.7 years ago by
stianlagstad
▴ 90
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