Showing : dexseq • reset
0
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237
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 10 weeks ago by ★ 4.4k • written 10 weeks ago by • 0
2
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1
reply
346
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How to design DEXSeq formula for multiple variables
DEXSeq
4 months ago • updated 3 months ago Sara • 0
3
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1
reply
384
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How to save the DEXSeq results
DEXSeq
updated 4 months ago by 42k • written 4 months ago by • 0
0
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0
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238
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
5 months ago Sara • 0
0
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3
replies
398
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 5 months ago by ★ 1.9k • written 5 months ago by • 0
0
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1
reply
312
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Adding columns to DEXSeqResults object
DEXSeq
updated 5 months ago by ★ 1.9k • written 5 months ago by • 0
0
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1
reply
425
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 months ago by 42k • written 5 months ago by • 0
0
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0
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272
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
6 months ago jean-christophe.helbling • 0
2
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4
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666
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
8 months ago • updated 7 months ago thomas.heigl.ibk • 0
0
votes
2
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539
views
Swimming downstream: transcript fold changes
DEXSeq stageR
10 months ago jbono ▴ 10
1
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1
reply
590
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
11 months ago NiKo ▴ 10
0
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3
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911
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 13 months ago by ★ 1.9k • written 13 months ago by • 0
0
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3
replies
1.1k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 13 months ago by 16k • written 14 months ago by • 0
0
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2
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769
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
13 months ago • updated 12 months ago yr542 • 0
8
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7
replies
2.2k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 15 months ago by ▴ 20 • written 23 months ago by ▴ 20
1
vote
5
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1.1k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 15 months ago by ★ 1.9k • written 15 months ago by • 0
0
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0
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552
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
15 months ago nick_brittain55 • 0
0
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0
replies
514
views
Error while performing DEXseq
DEXSeq
16 months ago vipul14 • 0
0
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0
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525
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
18 months ago Ben J ▴ 20
2
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2
replies
1.2k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
20 months ago Ben J ▴ 20
0
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0
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721
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 22 months ago by 42k • written 22 months ago by • 0
0
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1
reply
932
views
plotDEXSeq error?
DEXSeq dex
22 months ago barrypraveen • 0
1
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4
replies
1.1k
views
DEXseq batch removal
DEXSeq
updated 23 months ago by ★ 1.9k • written 23 months ago by ▴ 10
0
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0
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498
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.1 years ago Matthias Munz ▴ 20
0
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0
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613
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.1 years ago osieman52 • 0
1
vote
2
replies
975
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
2.1 years ago Delta._.43 ▴ 20
0
votes
1
reply
1.0k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.4 years ago • updated 2.3 years ago NIK • 0
0
votes
4
replies
1.8k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.3 years ago by ▴ 90 • written 2.4 years ago by • 0
0
votes
5
replies
2.2k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.5 years ago by • 0
7
votes
12
replies
3.7k
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 4 months ago by ▴ 30 • written 2.4 years ago by ▴ 380
3
votes
2
replies
1.2k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.5 years ago • updated 2.4 years ago Dakarai ▴ 10
1
vote
1
reply
792
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.5 years ago by ★ 1.9k • written 2.5 years ago by • 0
1
vote
2
replies
1.0k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.9 years ago • updated 2.7 years ago A ▴ 40
3
votes
3
replies
1.3k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.7 years ago by 42k • written 2.7 years ago by ▴ 120
0
votes
1
reply
1000
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.7 years ago by ★ 1.9k • written 3.0 years ago by • 0
1
vote
1
reply
1.3k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.7 years ago by ★ 1.9k • written 3.1 years ago by ▴ 10
2
votes
7
replies
1.5k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.1 years ago rbenel ▴ 40
0
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5
replies
1.5k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.1 years ago bioinformatic_trainee ▴ 10
1
vote
0
replies
1.1k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.2 years ago Matthias Munz ▴ 20
0
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0
replies
753
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.2 years ago n.tear ▴ 20
0
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0
replies
744
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.3 years ago Matthias Munz ▴ 20
1
vote
6
replies
1.8k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.3 years ago by ▴ 120 • written 3.5 years ago by ▴ 10
4
votes
5
replies
2.2k
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
3.4 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.0k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.5 years ago jbono ▴ 10
0
votes
2
replies
1.2k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.5 years ago Gaia • 0
3
votes
2
replies
1.2k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.6 years ago Angel ▴ 10
2
votes
2
replies
1.3k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.6 years ago n.tear ▴ 20
1
vote
1
reply
1.2k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3.7 years ago by ★ 1.9k • written 3.7 years ago by • 0
0
votes
2
replies
1.5k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
4.3 years ago • updated 3.9 years ago aleksandar.baburski.g • 0
1
vote
6
replies
4.2k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.9 years ago by ▴ 20 • written 9.5 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Poor dispersion fit in DESeq2 by Michael Love 42k
The fit (red line) doesn't matter because you have so many samples. Note there is almost no shrinkage. Besides that you may be intereste…
Answer: DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days p by Michael Love 42k
I'd recommend actually meeting with a local statistician to work out the analysis plan, or someone familiar with linear models in R. I h…
Answer: DESeq2 design and contrasts with 2 drug-treated and one control group by Michael Love 42k
> Now I am interested in comparing the DE genes between the resistant and acute groups, but I am unsure how to account for DMSO in that com…
Answer: Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentificat by Laurent Gatto 1.6k
Tthis happens because the sequence spectraVariable is expected to be an atomic vector or a List with elements of length 1, but it's not - s…
Comment: How should I run ssGSEA Hallmark Enrichment Analysis? by Ginny • 0
I think the other side of this question is that the non protein coding genes would be in the "background", they would influence the ranking…
Votes
Answer: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: addPatternDensity in 'qsea' takes too much time
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