Showing : DEXseq • reset
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My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
3 days ago cftattersfield • 0
0
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1
reply
351
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 6 months ago by ★ 4.6k • written 6 months ago by • 0
2
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1
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464
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How to design DEXSeq formula for multiple variables
DEXSeq
8 months ago • updated 7 months ago Sara • 0
3
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1
reply
550
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How to save the DEXSeq results
DEXSeq
updated 9 months ago by 43k • written 9 months ago by • 0
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0
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310
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
9 months ago Sara • 0
0
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3
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539
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 months ago by ★ 1.9k • written 9 months ago by • 0
0
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1
reply
417
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Adding columns to DEXSeqResults object
DEXSeq
updated 9 months ago by ★ 1.9k • written 9 months ago by • 0
0
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1
reply
695
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 9 months ago by 43k • written 9 months ago by • 0
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0
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359
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DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
10 months ago jean-christophe.helbling • 0
2
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4
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799
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
12 months ago • updated 11 months ago thomas.heigl.ibk • 0
0
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2
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639
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Swimming downstream: transcript fold changes
DEXSeq stageR
15 months ago jbono ▴ 10
1
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1
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683
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
15 months ago NiKo ▴ 10
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3
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1.0k
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 17 months ago by ★ 1.9k • written 17 months ago by • 0
0
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3
replies
1.3k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 17 months ago by 16k • written 18 months ago by • 0
0
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2
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912
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DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
18 months ago • updated 17 months ago yr542 • 0
8
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7
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2.4k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 19 months ago by ▴ 20 • written 2.3 years ago by ▴ 20
1
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5
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1.2k
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DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 19 months ago by ★ 1.9k • written 19 months ago by • 0
0
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0
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647
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
20 months ago nick_brittain55 • 0
0
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0
replies
579
views
Error while performing DEXseq
DEXSeq
20 months ago vipul14 • 0
0
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0
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577
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
23 months ago Ben J ▴ 20
2
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2
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1.5k
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.0 years ago • updated 24 months ago Ben J ▴ 20
0
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0
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806
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
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1
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1.0k
views
plotDEXSeq error?
DEXSeq dex
2.2 years ago barrypraveen • 0
1
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4
replies
1.2k
views
DEXseq batch removal
DEXSeq
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by ▴ 10
0
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0
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556
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.4 years ago Matthias Munz ▴ 20
0
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0
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674
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.5 years ago osieman52 • 0
1
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2
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1.1k
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DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
2.5 years ago Delta._.43 ▴ 20
0
votes
1
reply
1.1k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.7 years ago NIK • 0
0
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4
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2.0k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.7 years ago by ▴ 90 • written 2.8 years ago by • 0
0
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5
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2.3k
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DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.8 years ago by • 0
8
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12
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4.1k
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 8 months ago by ▴ 30 • written 2.8 years ago by ▴ 380
3
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2
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1.3k
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DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.8 years ago Dakarai ▴ 10
1
vote
1
reply
876
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.9 years ago by ★ 1.9k • written 2.9 years ago by • 0
1
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2
replies
1.2k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.2 years ago • updated 3.0 years ago A ▴ 40
3
votes
3
replies
1.4k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 120
0
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1
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1.1k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 3.0 years ago by ★ 1.9k • written 3.3 years ago by • 0
1
vote
1
reply
1.4k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3.0 years ago by ★ 1.9k • written 3.4 years ago by ▴ 10
2
votes
7
replies
1.6k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.4 years ago rbenel ▴ 40
0
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5
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1.6k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.5 years ago bioinformatic_trainee ▴ 10
1
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0
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1.3k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.5 years ago Matthias Munz ▴ 20
0
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0
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832
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.6 years ago n.tear ▴ 20
0
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0
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805
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DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.6 years ago Matthias Munz ▴ 20
1
vote
6
replies
1.9k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.6 years ago by ▴ 120 • written 3.8 years ago by ▴ 10
4
votes
5
replies
2.4k
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
3.8 years ago Matthias Munz ▴ 20
0
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0
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1.1k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.8 years ago jbono ▴ 10
0
votes
2
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1.3k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.9 years ago Gaia • 0
3
votes
2
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1.3k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.9 years ago Angel ▴ 10
2
votes
2
replies
1.4k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.0 years ago • updated 3.9 years ago n.tear ▴ 20
1
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1
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1.3k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 4.1 years ago by ★ 1.9k • written 4.1 years ago by • 0
0
votes
2
replies
1.6k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
4.6 years ago • updated 4.2 years ago aleksandar.baburski.g • 0
50 results • Page 1 of 1
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Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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