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DEXSeq
•
reset
0
votes
0
replies
86
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
11 days ago • updated 6 days ago
Sara
• 0
0
votes
3
replies
165
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 5 days ago by
Alejandro Reyes
★ 1.9k • written 17 days ago by
Alessia
• 0
0
votes
1
reply
154
views
Adding columns to DEXSeqResults object
DEXSeq
updated 17 days ago by
Alejandro Reyes
★ 1.9k • written 19 days ago by
Clyde
• 0
0
votes
1
reply
112
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 17 days ago by
Michael Love
41k • written 17 days ago by
09191919
• 0
0
votes
0
replies
134
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
7 weeks ago
jean-christophe.helbling
• 0
2
votes
4
replies
413
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
3 months ago • updated 9 weeks ago
thomas.heigl.ibk
• 0
0
votes
2
replies
371
views
Swimming downstream: transcript fold changes
DEXSeq
stageR
5 months ago
jbono
▴ 10
1
vote
1
reply
386
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
6 months ago
NiKo
▴ 10
0
votes
3
replies
657
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 8 months ago by
Alejandro Reyes
★ 1.9k • written 8 months ago by
Alice
• 0
0
votes
3
replies
780
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 8 months ago by
Hervé Pagès
16k • written 9 months ago by
anavmar1
• 0
0
votes
2
replies
561
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
8 months ago
yr542
• 0
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 10 months ago by
alexandresegers
▴ 20 • written 18 months ago by
jeremymsimon
▴ 20
1
vote
5
replies
855
views
DEXSeq output included non-exist exons
DEXSeq
exon_definition
exon
updated 10 months ago by
Alejandro Reyes
★ 1.9k • written 10 months ago by
zhangpeng1202
• 0
0
votes
0
replies
382
views
Recommendation sought for differential exon usage of a single gene
isofor
DEXSeq
DifferentialSplicing
11 months ago
nick_brittain55
• 0
0
votes
0
replies
397
views
Error while performing DEXseq
DEXSeq
11 months ago
vipul14
• 0
0
votes
0
replies
424
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
13 months ago
Ben J
• 0
0
votes
2
replies
900
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
15 months ago
Ben J
• 0
0
votes
0
replies
576
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 17 months ago by
Michael Love
41k • written 17 months ago by
barrypraveen
• 0
0
votes
1
reply
801
views
plotDEXSeq error?
DEXSeq
dex
17 months ago
barrypraveen
• 0
1
vote
4
replies
935
views
DEXseq batch removal
DEXSeq
updated 19 months ago by
Alejandro Reyes
★ 1.9k • written 19 months ago by
ta_awwad
▴ 10
0
votes
0
replies
420
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
20 months ago
Matthias Munz
▴ 10
0
votes
0
replies
498
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
21 months ago
osieman52
• 0
1
vote
2
replies
827
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
21 months ago
Delta._.43
▴ 20
0
votes
1
reply
839
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
23 months ago
NIK
• 0
0
votes
4
replies
1.4k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 23 months ago by
jeroen.gilis
▴ 90 • written 2.0 years ago by
phoebe1354
• 0
0
votes
5
replies
1.9k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.1 years ago by
maslane
• 0
6
votes
11
replies
3.0k
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 13 months ago by
EChambers
• 0 • written 2.0 years ago by
Matthew Thornton
▴ 350
3
votes
2
replies
947
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
2.1 years ago • updated 2.0 years ago
Dakarai
▴ 10
1
vote
1
reply
651
views
Increased number of exons in DEXSeq
DEXSeq
exon
updated 2.1 years ago by
Alejandro Reyes
★ 1.9k • written 2.1 years ago by
jochen
• 0
1
vote
2
replies
866
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.5 years ago • updated 2.3 years ago
A
▴ 40
3
votes
3
replies
1.1k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2
DEXseq
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
k.vitting.seerup
▴ 120
0
votes
1
reply
842
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.3 years ago by
Alejandro Reyes
★ 1.9k • written 2.6 years ago by
Hahsooni
• 0
1
vote
1
reply
1.1k
views
DTU using DEXSeq (time series data with condition factor)
DTU
DEXSeq
RNADTU
updated 2.3 years ago by
Alejandro Reyes
★ 1.9k • written 2.7 years ago by
Nirad
▴ 10
2
votes
7
replies
1.3k
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
2.7 years ago
rbenel
▴ 40
0
votes
5
replies
1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
2.7 years ago
bioinformatic_trainee
▴ 10
0
votes
0
replies
827
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures
DEXSeq
2.8 years ago
Matthias Munz
▴ 10
0
votes
0
replies
635
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
2.8 years ago
n.tear
▴ 20
0
votes
0
replies
636
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.9 years ago
Matthias Munz
▴ 10
1
vote
6
replies
1.5k
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
updated 2.9 years ago by
k.vitting.seerup
▴ 120 • written 3.1 years ago by
jbono
▴ 10
4
votes
5
replies
1.9k
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
3.0 years ago
Matthias Munz
▴ 10
0
votes
0
replies
873
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
3.1 years ago
jbono
▴ 10
0
votes
2
replies
999
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
3.1 years ago
Gaia
• 0
3
votes
2
replies
1.0k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.2 years ago
Angel
▴ 10
2
votes
2
replies
1.2k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq
JunctionSeq
RNAseq
QoRTs
3.2 years ago
n.tear
▴ 20
1
vote
1
reply
988
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3.3 years ago by
Alejandro Reyes
★ 1.9k • written 3.3 years ago by
Anubhav
• 0
0
votes
2
replies
1.2k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
3.9 years ago • updated 3.5 years ago
aleksandar.baburski.g
• 0
1
vote
6
replies
4.0k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.5 years ago by
rohitsatyam102
▴ 20 • written 9.1 years ago by
ywu
• 0
0
votes
2
replies
1.5k
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq
estimatedispersions
updated 3.5 years ago by
rohitsatyam102
▴ 20 • written 6.3 years ago by
brand
• 0
6
votes
7
replies
1.7k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq
DESeq2
updated 3.4 years ago by
Michael Love
41k • written 3.5 years ago by
rohitsatyam102
▴ 20
0
votes
2
replies
889
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 3.8 years ago by
Simon Anders
★ 3.7k • written 3.8 years ago by
lu.la
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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