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0
votes
3
answers
106
views
3
answers
Pathview -- Error in korg[ridx, coln] : subscript out of bounds
pathview subscript out of bounds tutorial korg written 9 days ago by aacevedo • 0 • updated 6 minutes ago by Luo Weijun • 1.4k
0
votes
1
answer
9
views
1
answer
Draw volcano plot by modifying contrast matrix (lumi package)
design and contrast matrix volcanoplot written 36 minutes ago by marongiu.luigi • 0 • updated 11 minutes ago by James W. MacDonald ♦ 44k
0
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0
answers
6
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0
answers
NA values of count matrix in class DESeqDataSet
rna-seq recount written 30 minutes ago by maleknias • 0
0
votes
2
answers
34
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2
answers
DESeq2 Which gene used to normalize?
normalization deseq2 R written 3 hours ago by michi.s • 0 • updated 1 hour ago by Steve Lianoglou ♦ 12k
0
votes
1
answer
16
views
1
answer
Windows 10 openCyto Install: installation path not writeable, unable to update packages: boot, Matrix, mgcv
opencyto bioclite package installation written 1 hour ago by Robert Baer • 70 • updated 1 hour ago by ekwame001 • 0
9
votes
11
answers
2.2k
views
16 follow
11
answers
readCufflinks problem with extdata
cummerbund written 12 weeks ago by biakemi • 30 • updated 1 hour ago by markus.ball • 0
1
vote
1
answer
55
views
1
answer
Differential expression of nomalised and log2 transformed data in limma
limma differential gene expression lmfit model.matrix written 3 days ago by stinehedensted • 0
0
votes
0
answers
27
views
0
answers
Pheatmap clustering and row annotation
R pheatmap cutree written 6 hours ago by meseretbrihanu • 0
1
vote
1
answer
66
views
1
answer
POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
txdb.hsapiens.ucsc.hg19.knowngene written 13 hours ago by tangming2005 • 70 • updated 7 hours ago by jma1991 • 30
1
vote
1
answer
31
views
1
answer
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
annotationdbi deseq2 tximport written 13 hours ago by prab4th • 0 • updated 12 hours ago by Johannes Rainer • 960
0
votes
1
answer
47
views
1
answer
DESeq2 Dispersion Shrinkage - more samples is better?
deseq2 dds written 1 day ago by rrcutler • 30 • updated 23 hours ago by Michael Love ♦ 13k
1
vote
2
answers
42
views
2
answers
Gene Size using GenomicFeatures
genomicfeatures gene length gene size written 1 day ago by ehimelbl • 0
0
votes
1
answer
50
views
1
answer
Different PCA plots using rlog and vsd on the same data set
deseq2 pca rlog variancestabilizingtransformation plotpca written 1 day ago by lirongrossmann • 0 • updated 1 day ago by Michael Love ♦ 13k
0
votes
0
answers
40
views
0
answers
Error: unable to find an inherited method for function searchSeq for signature matrix
tfbstools jaspar pwm written 2 days ago by chrisclarkson100 • 30
1
vote
1
answer
38
views
1
answer
Could not find function "makeTranscriptDbFromGFF"
annotation genomicfeatures gff maketranscriptdbfromgff written 1 day ago by Gary • 0 • updated 1 day ago by Michael Lawrence ♦ 9.6k
3
votes
2
answers
56
views
2
answers
limma-trend with random effects and/or array weights
limma duplicatecorrelation arrayweights limma-trend written 1 day ago by maltethodberg • 40 • updated 1 day ago by Gordon Smyth ♦ 31k
0
votes
0
answers
28
views
0
answers
Error executing flowcore vignette
flowcore software error vignette written 1 day ago by Robert Baer • 70
0
votes
1
answer
42
views
1
answer
appointing a new maintainer for my package
bioconductor written 2 days ago by christophbernau • 0 • updated 1 day ago by Martin Morgan ♦♦ 20k
0
votes
1
answer
50
views
1
answer
How to plot Oncoplot with out sorting
maftools written 5 days ago by seeker • 0 • updated 2 days ago by anand_mt • 60
1
vote
1
answer
50
views
1
answer
DESeq2 Design Formula for Time Series Experiment
deseq2 written 2 days ago by gkuffel • 10 • updated 2 days ago by David Requena • 0
2
votes
1
answer
61
views
1
answer
Obtaining transcript names in RSEM
tximport rsem written 2 days ago by deena • 0 • updated 2 days ago by Michael Love ♦ 13k
3
votes
2
answers
86
views
2
answers
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq written 6 days ago by David Requena • 0
10
votes
1
answer
1.5k
views
5 follow
1
answer
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq limma edger deseq2 voom written 2.3 years ago by Sean Davis ♦ 20k • updated 2 days ago by Paul Harrison • 60
0
votes
1
answer
32
views
1
answer
R session crash with SGSeq::convertToTxFeatures
sgseq txdb crash maketxdbfrombiomart txfeatures written 2 days ago by oolongoni • 10 • updated 2 days ago by Leonard Goldstein • 20
0
votes
1
answer
40
views
1
answer
Error downloading the package
download tcga tcgabiolinks written 2 days ago by sup230 • 10 • updated 2 days ago by James W. MacDonald ♦ 44k
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