Showing : dexseq • reset
0
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3
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162
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 4 days ago by ★ 1.9k • written 16 days ago by • 0
0
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0
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83
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
10 days ago • updated 5 days ago Sara • 0
0
votes
1
reply
153
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Adding columns to DEXSeqResults object
DEXSeq
updated 16 days ago by ★ 1.9k • written 18 days ago by • 0
0
votes
1
reply
111
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 16 days ago by 41k • written 16 days ago by • 0
0
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0
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133
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DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
7 weeks ago jean-christophe.helbling • 0
2
votes
4
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410
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
3 months ago • updated 9 weeks ago thomas.heigl.ibk • 0
0
votes
2
replies
367
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Swimming downstream: transcript fold changes
DEXSeq stageR
5 months ago jbono ▴ 10
1
vote
1
reply
386
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
6 months ago NiKo ▴ 10
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2
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560
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DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
8 months ago yr542 • 0
0
votes
3
replies
656
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 8 months ago by ★ 1.9k • written 8 months ago by • 0
0
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3
replies
778
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Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 8 months ago by 16k • written 9 months ago by • 0
8
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7
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1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 18 months ago by ▴ 20
1
vote
5
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854
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
0
votes
0
replies
382
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
11 months ago nick_brittain55 • 0
0
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0
replies
395
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Error while performing DEXseq
DEXSeq
11 months ago vipul14 • 0
6
votes
11
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3.0k
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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 • 0 • written 2.0 years ago by ▴ 350
0
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0
replies
423
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
13 months ago Ben J • 0
0
votes
2
replies
898
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
15 months ago Ben J • 0
1
vote
15
replies
3.5k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 16 months ago by • 0 • written 7.0 years ago by • 0
0
votes
0
replies
575
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 17 months ago by 41k • written 17 months ago by • 0
0
votes
1
reply
800
views
plotDEXSeq error?
DEXSeq dex
17 months ago barrypraveen • 0
1
vote
4
replies
934
views
DEXseq batch removal
DEXSeq
updated 18 months ago by ★ 1.9k • written 19 months ago by ▴ 10
0
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0
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419
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
20 months ago Matthias Munz ▴ 10
1
vote
2
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2.0k
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 20 months ago by ▴ 10 • written 4.8 years ago by ▴ 10
0
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0
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497
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
21 months ago osieman52 • 0
1
vote
2
replies
826
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
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1
reply
837
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 ▴ 90 • written 2.0 years ago by • 0
3
votes
2
replies
946
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
0
votes
5
replies
1.9k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.1 years ago by • 0
1
vote
1
reply
651
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.1 years ago by ★ 1.9k • written 2.1 years ago by • 0
1
vote
2
replies
865
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.4 years ago • updated 2.3 years ago A ▴ 40
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 ★ 1.9k • written 2.7 years ago by ▴ 10
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 ★ 1.9k • written 2.6 years ago by • 0
3
votes
3
replies
1.1k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.3 years ago by 41k • written 2.3 years ago by ▴ 120
3
votes
2
replies
1.9k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq fit matrix warning
updated 2.5 years ago by • 0 • written 7.2 years ago by ★ 1.5k
2
votes
7
replies
1.3k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
2.7 years ago rbenel ▴ 40
3
votes
3
replies
1.7k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 2.7 years ago by ▴ 20 • written 4.1 years ago by ▴ 20
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
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0
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827
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.8 years ago Matthias Munz ▴ 10
0
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0
replies
634
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
634
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 ▴ 120 • written 3.1 years ago by ▴ 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
998
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.1 years ago Gaia • 0
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
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
1
vote
1
reply
988
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3.3 years ago by ★ 1.9k • written 3.3 years ago by • 0
6
votes
7
replies
1.7k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 3.4 years ago by 41k • written 3.5 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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