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DEXSEq
•
reset
0
votes
1
reply
73
views
Testing subgroup-specific interactions in DEXSeq
DEXSeq
RNASeqData
Transcriptomics
10 days ago • updated 6 days ago
palanikumars2
• 0
0
votes
1
reply
371
views
Make DEXSeq plot normal scale
DEXSeq
Dexseq
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
Rico
• 0
4
votes
6
replies
1.7k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
Elijah
• 0
0
votes
0
replies
423
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing
RNASeqData
DEXSeq
13 months ago
cftattersfield
• 0
0
votes
1
reply
617
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
2406691063
• 0
2
votes
1
reply
892
views
How to design DEXSeq formula for multiple variables
DEXSeq
21 months ago • updated 20 months ago
Sara
• 0
3
votes
1
reply
985
views
How to save the DEXSeq results
DEXSeq
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Sara
• 0
0
votes
0
replies
609
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
22 months ago
Sara
• 0
0
votes
3
replies
953
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 22 months ago by
Alejandro Reyes
★ 1.9k • written 22 months ago by
Alessia
• 0
0
votes
1
reply
763
views
Adding columns to DEXSeqResults object
DEXSeq
updated 22 months ago by
Alejandro Reyes
★ 1.9k • written 22 months ago by
Clyde
• 0
0
votes
1
reply
1.7k
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 22 months ago by
Michael Love
43k • written 22 months ago by
09191919
• 0
0
votes
0
replies
553
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
23 months ago
jean-christophe.helbling
• 0
2
votes
4
replies
1.3k
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
2.1 years ago • updated 24 months ago
thomas.heigl.ibk
• 0
0
votes
2
replies
904
views
Swimming downstream: transcript fold changes
DEXSeq
stageR
2.3 years ago
jbono
▴ 10
1
vote
1
reply
1.0k
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
2.3 years ago
NiKo
▴ 10
0
votes
3
replies
1.5k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 2.5 years ago by
Alejandro Reyes
★ 1.9k • written 2.5 years ago by
Alice
• 0
0
votes
3
replies
1.8k
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 2.5 years ago by
Hervé Pagès
16k • written 2.6 years ago by
anavmar1
• 0
0
votes
2
replies
1.4k
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
2.5 years ago
yr542
• 0
8
votes
7
replies
3.3k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 2.6 years ago by
alexandresegers
▴ 20 • written 3.3 years ago by
jeremymsimon
▴ 20
1
vote
5
replies
1.6k
views
DEXSeq output included non-exist exons
DEXSeq
exon_definition
exon
updated 2.6 years ago by
Alejandro Reyes
★ 1.9k • written 2.7 years ago by
zhangpeng1202
• 0
0
votes
0
replies
886
views
Recommendation sought for differential exon usage of a single gene
isofor
DEXSeq
DifferentialSplicing
2.7 years ago
nick_brittain55
• 0
0
votes
0
replies
769
views
Error while performing DEXseq
DEXSeq
2.7 years ago
vipul14
• 0
0
votes
0
replies
817
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
3.0 years ago
Ben J
▴ 20
2
votes
2
replies
2.0k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
3.1 years ago • updated 3.0 years ago
Ben J
▴ 20
0
votes
0
replies
1.1k
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
barrypraveen
• 0
0
votes
1
reply
1.3k
views
plotDEXSeq error?
DEXSeq
dex
3.3 years ago • updated 3.2 years ago
barrypraveen
• 0
1
vote
4
replies
1.6k
views
DEXseq batch removal
DEXSeq
updated 3.4 years ago by
Alejandro Reyes
★ 1.9k • written 3.4 years ago by
ta_awwad
▴ 10
0
votes
0
replies
785
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
3.5 years ago
Matthias Munz
▴ 20
0
votes
0
replies
881
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
3.5 years ago
osieman52
• 0
1
vote
2
replies
1.5k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
3.5 years ago
Delta._.43
▴ 20
0
votes
1
reply
1.5k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
3.8 years ago • updated 3.7 years ago
NIK
• 0
0
votes
4
replies
2.8k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 3.8 years ago by
jeroen.gilis
▴ 100 • written 3.8 years ago by
phoebe1354
• 0
0
votes
5
replies
2.7k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 6.9 years ago by
maslane
• 0
8
votes
12
replies
5.2k
views
DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq)
DEXSeq
updated 21 months ago by
Marek Gierlinski
▴ 30 • written 3.9 years ago by
Matthew Thornton
▴ 390
3
votes
2
replies
1.9k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
3.9 years ago • updated 3.8 years ago
Dakarai
▴ 10
1
vote
1
reply
1.1k
views
Increased number of exons in DEXSeq
DEXSeq
exon
updated 3.9 years ago by
Alejandro Reyes
★ 1.9k • written 3.9 years ago by
jochen
• 0
1
vote
2
replies
1.6k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
4.3 years ago • updated 4.1 years ago
A
▴ 60
3
votes
3
replies
1.8k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2
DEXseq
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
k.vitting.seerup
▴ 120
0
votes
1
reply
1.4k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 4.1 years ago by
Alejandro Reyes
★ 1.9k • written 4.4 years ago by
Hahsooni
• 0
1
vote
1
reply
1.8k
views
DTU using DEXSeq (time series data with condition factor)
DTU
DEXSeq
RNADTU
updated 4.1 years ago by
Alejandro Reyes
★ 1.9k • written 4.5 years ago by
Nirad
▴ 10
2
votes
7
replies
2.1k
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
4.5 years ago
rbenel
▴ 50
0
votes
5
replies
2.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
4.5 years ago
bioinformatic_trainee
▴ 10
1
vote
0
replies
1.7k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures
DEXSeq
4.6 years ago
Matthias Munz
▴ 20
0
votes
0
replies
1.0k
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
4.6 years ago
n.tear
▴ 20
0
votes
0
replies
1.1k
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
4.7 years ago
Matthias Munz
▴ 20
1
vote
6
replies
2.6k
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
updated 4.7 years ago by
k.vitting.seerup
▴ 120 • written 4.9 years ago by
jbono
▴ 10
4
votes
5
replies
3.1k
views
DEXSeq: What's the best way to map an exon counting bin, e.g. E002 to exon(s) or position in transcript(s)
DEXSeq
4.8 years ago
Matthias Munz
▴ 20
0
votes
0
replies
1.4k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
4.9 years ago
jbono
▴ 10
0
votes
2
replies
1.7k
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
4.9 years ago
Gaia
• 0
3
votes
2
replies
1.7k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
5.0 years ago
Angel
▴ 10
364 results • Page
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Comment: Question on processing compound protein groups in limpa
by
JKim
• 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa
by
Gordon Smyth
53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input
by
Gordon Smyth
53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2
by
a2a2hset32aa
• 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Comment: Deadline Extended: EuroBioC2026 Call for Abstracts
by
a2a2hset32aa
• 0
Attending EuroBioC2026 is an excellent way for researchers to explore the intersection of technology and biology. For those seeking high qu…
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Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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