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DEXseq
•
reset
0
votes
2
replies
1.3k
views
Inclusion of non-coding portions of transcripts (UTR-regions and introns) within the DEX-seq dataset
dexseq
deseq2
differential exon usage
updated 3 days ago by
Pat
• 0 • written 9.4 years ago by
ste.depo
▴ 10
0
votes
1
reply
108
views
Testing subgroup-specific interactions in DEXSeq
DEXSeq
RNASeqData
Transcriptomics
25 days ago • updated 22 days ago
palanikumars2
• 0
0
votes
2
replies
1.4k
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq
splicing
RNAseq
DEXSeq
written 6.3 years ago by
stuart
▴ 10
0
votes
1
reply
380
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
1.8k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 11 months ago by
ATpoint
★ 5.0k • written 12 months ago by
Elijah
• 0
0
votes
0
replies
445
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
626
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
2406691063
• 0
2
votes
1
reply
902
views
How to design DEXSeq formula for multiple variables
DEXSeq
22 months ago • updated 21 months ago
Sara
• 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
1
reply
1.0k
views
How to save the DEXSeq results
DEXSeq
updated 22 months ago by
Michael Love
43k • written 22 months ago by
Sara
• 0
0
votes
3
replies
972
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 22 months ago by
Alejandro Reyes
★ 1.9k • written 23 months ago by
Alessia
• 0
0
votes
0
replies
618
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
22 months ago
Sara
• 0
0
votes
1
reply
780
views
Adding columns to DEXSeqResults object
DEXSeq
updated 23 months ago by
Alejandro Reyes
★ 1.9k • written 23 months ago by
Clyde
• 0
0
votes
1
reply
1.8k
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 23 months ago by
Michael Love
43k • written 23 months ago by
09191919
• 0
0
votes
0
replies
559
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
2.0 years 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 2.0 years ago
thomas.heigl.ibk
• 0
0
votes
2
replies
911
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
2.4 years ago
NiKo
▴ 10
0
votes
2
replies
1.4k
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
2.6 years ago • updated 2.5 years ago
yr542
• 0
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
1.9k
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 2.6 years ago by
Hervé Pagès
16k • written 2.6 years ago by
anavmar1
• 0
8
votes
7
replies
3.3k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 2.7 years ago by
alexandresegers
▴ 20 • written 3.4 years ago by
jeremymsimon
▴ 20
1
vote
5
replies
1.7k
views
DEXSeq output included non-exist exons
DEXSeq
exon_definition
exon
updated 2.7 years ago by
Alejandro Reyes
★ 1.9k • written 2.7 years ago by
zhangpeng1202
• 0
0
votes
0
replies
893
views
Recommendation sought for differential exon usage of a single gene
isofor
DEXSeq
DifferentialSplicing
2.8 years ago
nick_brittain55
• 0
0
votes
0
replies
777
views
Error while performing DEXseq
DEXSeq
2.8 years ago
vipul14
• 0
0
votes
0
replies
827
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 `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
3.1 years ago
Ben J
▴ 20
1
vote
15
replies
4.7k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 3.2 years ago by
Zhuqiang
• 0 • written 8.9 years ago by
cpsosa0006
• 0
0
votes
0
replies
1.1k
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
barrypraveen
• 0
0
votes
1
reply
1.3k
views
plotDEXSeq error?
DEXSeq
dex
3.3 years ago
barrypraveen
• 0
1
vote
4
replies
1.6k
views
DEXseq batch removal
DEXSeq
updated 3.4 years ago by
Alejandro Reyes
★ 1.9k • written 3.4 years ago by
ta_awwad
▴ 10
0
votes
0
replies
800
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
3.5 years ago
Matthias Munz
▴ 20
1
vote
2
replies
2.6k
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 3.6 years ago by
ta_awwad
▴ 10 • written 6.6 years ago by
bruce.hayward
▴ 10
0
votes
0
replies
887
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
3.6 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
3.6 years ago
Delta._.43
▴ 20
0
votes
1
reply
1.6k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
3.8 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 3.9 years ago by
phoebe1354
• 0
3
votes
2
replies
2.0k
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
Dakarai
▴ 10
0
votes
5
replies
2.7k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 6.9 years ago by
maslane
• 0
1
vote
1
reply
1.1k
views
Increased number of exons in DEXSeq
DEXSeq
exon
updated 4.0 years ago by
Alejandro Reyes
★ 1.9k • written 4.0 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
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
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
3
votes
3
replies
1.8k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2
DEXseq
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
k.vitting.seerup
▴ 120
3
votes
2
replies
2.6k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq
fit
matrix
warning
updated 4.3 years ago by
koushik
• 0 • written 9.1 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
7
replies
2.2k
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
4.6 years ago • updated 4.5 years ago
rbenel
▴ 50
3
votes
3
replies
2.8k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq
log2foldchange
Tutorial
updated 4.5 years ago by
rohitsatyam102
▴ 20 • written 5.9 years ago by
tmvarsha
▴ 20
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
4.6 years ago
bioinformatic_trainee
▴ 10
1
vote
0
replies
1.8k
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
4.7 years ago
n.tear
▴ 20
364 results • Page
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Thank you very much for taking the time to offer your advice and comments. I truly appreciate them. Best regards, J Kim
Answer: Convergence Issues and Model Selection DESeq2
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43k
You could try `glmGamPoi` fitting via `fitType`: https://github.com/thelovelab/DESeq2/blob/devel/man/DESeq.Rd#L10 This is a more rece…
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Answer: Quick two questions on limpa
Answer: Quick two questions on limpa
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