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dexseq
•
reset
0
votes
0
replies
1.0k
views
problem with DexSeq for only two isoform cases
dexseq
8.6 years ago
Ays
• 0
3
votes
2
replies
2.4k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq
fit
matrix
warning
updated 3.8 years ago by
koushik
• 0 • written 8.6 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
7
replies
2.2k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq
dexseq
updated 8.6 years ago by
Alejandro Reyes
★ 1.9k • written 8.6 years ago by
tofukaj
• 0
6
votes
3
replies
3.6k
views
plotDEXSeq error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values
dexseq
differential exon usage
8.6 years ago
fizer
▴ 40
0
votes
1
reply
1.5k
views
Appropriate to apply RUVSeq to exon bin counts for DEXSeq?
dexseq
ruvseq
rnaseq
updated 8.6 years ago by
davide risso
▴ 980 • written 8.7 years ago by
Cornwell, Adam
▴ 110
3
votes
4
replies
4.1k
views
Simultaneously adding two different covariates in the model gives error in DESeq2.
deseq2
dexseq
rnaseq
differential gene expression
differential exon usage
updated 8.7 years ago by
Michael Love
43k • written 8.7 years ago by
fizer
▴ 40
2
votes
1
reply
826
views
"condition" factor name is hardcoded
DEXSeq
8.7 years ago
bjoern.gruening
• 0
0
votes
1
reply
1.7k
views
JunctionSeq/DEXSeq: Dispersion plot looks strange (but is fine in DESeq2)
deseq2
junctionseq
dexseq
estimatedispersions
rnaseq
updated 8.7 years ago by
Steve Lianoglou
★ 13k • written 8.7 years ago by
l.frank
• 0
1
vote
2
replies
2.7k
views
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
8.8 years ago
Mthabisi Moyo
▴ 40
1
vote
1
reply
1.4k
views
exonBaseMean calculation in DEXSeq
dexseq
8.9 years ago
nobishvarghese
• 0
0
votes
1
reply
1.1k
views
Inclusion of non-coding portions of transcripts (UTR-regions and introns) within the DEX-seq dataset
dexseq
deseq2
differential exon usage
updated 7 weeks ago by
Tim
• 0 • written 8.9 years ago by
ste.depo
▴ 10
0
votes
0
replies
1.3k
views
DEXSeq error: erro in dexseq_count.py
dexseq_count
dexseq
htseqcounts
9.0 years ago
as1023
• 0
16
votes
6
replies
4.1k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR
limma
diffSplice
DEXSeq
updated 9.1 years ago by
Charity Law
▴ 90 • written 9.1 years ago by
maltethodberg
▴ 180
0
votes
8
replies
1.8k
views
No significant hits!
dexseq
updated 9.1 years ago by
Alejandro Reyes
★ 1.9k • written 9.1 years ago by
saudpabita
• 0
0
votes
2
replies
1.1k
views
DEXSeq subscript out of bonds error
dexseq
9.2 years ago
vinko.palada
• 0
4
votes
7
replies
2.2k
views
assigning differential exons to trascripts
dexseq
rsem
differential exon usage
differential gene expression
updated 9.2 years ago by
James W. MacDonald
68k • written 9.2 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.3k
views
DEXSeq: while running dexseq_count.py, I am getting error messages
dexseq
dexseq_count
9.2 years ago
wunglee2019
• 0
1
vote
2
replies
1.6k
views
DEXseq for alternate promoter usage
dexseq
promoter
utr
updated 9.2 years ago by
Alejandro Reyes
★ 1.9k • written 9.2 years ago by
joan.hooper
• 0
1
vote
2
replies
1.5k
views
DEXSeq. Error: could not find function "DEXSeqDataSetFromHTSeq"
dexseq
9.3 years ago
peter.thorpe
• 0
0
votes
1
reply
1.8k
views
DEXSeq and shrinkage diagnostic : Comparison between results in plotDispEsts( dxd )
dexseq
estimatedispersions
updated 9.4 years ago by
Wolfgang Huber
★ 13k • written 9.4 years ago by
julie.sedbon
• 0
0
votes
1
reply
1.5k
views
interpreting dispersion estimation in dexseq
deseq2
dexseq
estimatedispersions
updated 9.4 years ago by
Wolfgang Huber
★ 13k • written 9.4 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
1.0k
views
dexseq_prepare_annotation gives an empty gff file
dexseq
prepare annotation
empty gff
9.4 years ago
sakura.nussbaum
▴ 10
1
vote
3
replies
2.0k
views
DEXSeq warnings for millions of reads
DEXSeq
warnings
dexseq_count
updated 9.4 years ago by
Darya Vanichkina
▴ 130 • written 9.4 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
12
replies
3.8k
views
Error in strsplit() : non-character argument - using DEXSeq
dexseq_count
DEXSeqDataSetFromHTSeq
DEXSeq
strsplit
updated 9.4 years ago by
aditi
▴ 20 • written 9.4 years ago by
sakura.nussbaum
▴ 10
1
vote
6
replies
2.4k
views
Error: could not find function "HTSeqCounts"
HTSeq
HTSeqCounts
Could not find function
DEXSeq
updated 9.4 years ago by
Martin Morgan
25k • written 9.4 years ago by
sakura.nussbaum
▴ 10
0
votes
0
replies
968
views
How can I use RefGene.gtf with DEXSeq
dexseq
9.4 years ago
julie.sedbon
• 0
2
votes
3
replies
2.5k
views
dexseq_count.py 'SAM optional field tag NH not found'
dexseq
updated 9.4 years ago by
juls.jaeger
• 0 • written 9.8 years ago by
Dimitra Alexopoulou
▴ 30
2
votes
2
replies
1.4k
views
Subset DEXSeqDataSet In DEXSeq
dexseq
9.5 years ago
adelmane
▴ 20
3
votes
6
replies
4.0k
views
DEXSeq Error: unable to find an inherited method for function ‘mcols’ for signature ‘"matrix"’
DEXSeq
updated 9.5 years ago by
Alejandro Reyes
★ 1.9k • written 9.5 years ago by
MedwayC
• 0
1
vote
5
replies
1.8k
views
DEXSeq: large pvalue for expected differentially expressed exons
dexseq
updated 9.5 years ago by
Alejandro Reyes
★ 1.9k • written 9.5 years ago by
Chao-Jen Wong
▴ 40
0
votes
7
replies
4.5k
views
DEXSeq Error in estimateExonFoldChanges: the matrix is either rank-deficient or indefinite
dexseq
estimateexonfoldchanges
updated 9.5 years ago by
Alejandro Reyes
★ 1.9k • written 9.5 years ago by
aditi
▴ 20
0
votes
8
replies
2.6k
views
DEXSeqHTML Output Trouble
dexseq
dexseqhtml
9.5 years ago
skasowitz
• 0
1
vote
1
reply
1.3k
views
DESeq2 analysis with multiple biological parameters
deseq2
dexseq
multiple factor design
multifactorial design
updated 9.5 years ago by
Michael Love
43k • written 9.5 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
3
replies
1.4k
views
DEXSeq ignore non-coding regions
dexseq
updated 9.6 years ago by
Alejandro Reyes
★ 1.9k • written 9.6 years ago by
igor
▴ 50
0
votes
0
replies
1.3k
views
Regarding DEXseq input file
dexseq
9.6 years ago
thellambure_hettige
• 0
0
votes
2
replies
1.5k
views
DEXSeq on time series - how to set up models
DEXSeq
timecourse
rna-seq
differential exon usage
updated 9.6 years ago by
Alejandro Reyes
★ 1.9k • written 9.6 years ago by
MedwayC
• 0
0
votes
1
reply
1.3k
views
DEXSeq estimateExonFoldChanges breaks samples' names and counts relation
software error
dexseq
estimateexonfoldchanges
updated 9.6 years ago by
Alejandro Reyes
★ 1.9k • written 9.6 years ago by
gmerino
▴ 20
2
votes
3
replies
1.9k
views
DEXSeq error upon executing testForDEU()
dexseq
updated 9.6 years ago by
Alejandro Reyes
★ 1.9k • written 9.6 years ago by
t.kuilman
▴ 170
0
votes
0
replies
1.1k
views
DEXSeq explanation on the output
dexseq
9.6 years ago
jarod_v6@libero.it
▴ 40
1
vote
4
replies
1.4k
views
DEXSeq count differential exons
dexseq
9.6 years ago
jarod_v6@libero.it
▴ 40
0
votes
2
replies
1.7k
views
Error with DEXSeqDataSet object after performing pre-filter
DEXSeq
rownames
pre-filtering
updated 9.6 years ago by
Wolfgang Huber
★ 13k • written 9.6 years ago by
arom2
• 0
0
votes
4
replies
2.3k
views
DEXSeq: dexseq_count.py - Failure parsing GFF attribute line
DEXSeq
updated 9.7 years ago by
Alejandro Reyes
★ 1.9k • written 9.7 years ago by
lcscs12345
• 0
0
votes
5
replies
3.1k
views
NA in padj in the DEXSeq package
dexseq
padj
9.7 years ago
gil.hornung
• 0
0
votes
0
replies
1.1k
views
line colors plotRangesLinkedToData
ggbio
ggplot2
dexseq
9.7 years ago
Alejandro Reyes
★ 1.9k
0
votes
4
replies
2.5k
views
Error in exp(alleffects) : non-numeric argument to mathematical function
dexseq
estimateExonFoldChanges
updated 9.8 years ago by
Alejandro Reyes
★ 1.9k • written 9.8 years ago by
Mehmet Ilyas Cosacak
• 0
0
votes
3
replies
2.0k
views
DEXSeqHTML parallelization error
Parallel
DEXSeq
DEXSeqHTML
9.8 years ago
Neel Aluru
▴ 460
2
votes
4
replies
2.1k
views
DEXSeqDataSet example code
DEXSeq
updated 9.8 years ago by
zb.picb
• 0 • written 9.8 years ago by
pensona
▴ 20
0
votes
2
replies
1.9k
views
DEXSeq exon usage values in result table
DEXSeq
differential exon usage
exon usage
updated 9.8 years ago by
Alejandro Reyes
★ 1.9k • written 9.8 years ago by
biominer
▴ 10
0
votes
1
reply
1.4k
views
estimateDispersions fails even with fitType local
deseq2
dexseq
alternative splicing
updated 9.8 years ago by
Michael Love
43k • written 9.8 years ago by
sahiilseth
• 0
2
votes
2
replies
1.9k
views
DEXSeq: DEXSeqHTML, plotDEXSeq and interaction tests
dexseq
updated 9.8 years ago by
Alejandro Reyes
★ 1.9k • written 9.8 years ago by
Joseph Bundy
▴ 20
363 results • Page
4 of 8
Recent ...
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Answer: DESeq2 used with zinbwave weights - Differences on contrasts calculations
by
eja.gsee.r.m
• 0
Hi your issue with DESeq2 contrasts and zinbwave weights sounds like it might stem from how weights are integrated during the different con…
Comment: How to analyze Affy data, CEL files not available
by
eja.gsee.r.m
• 0
When analyzing data without raw files like Bobby MAS expression measures t important to work within the limits of the available informatio…
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
Gordon Smyth
53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
by
Michael Love
43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Comment: Average biological replicates in RNA-seq
by
boczniak767
▴ 740
@atpoint Should I first standardise data and then average replicates?
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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