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
29 days ago cftattersfield • 0
0
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1
reply
376
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 7 months ago by ★ 4.7k • written 7 months ago by • 0
2
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1
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517
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How to design DEXSeq formula for multiple variables
DEXSeq
9 months ago • updated 8 months ago Sara • 0
3
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1
reply
607
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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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328
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
10 months ago Sara • 0
0
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3
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567
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
0
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1
reply
445
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Adding columns to DEXSeqResults object
DEXSeq
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
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1
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777
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 10 months ago by 43k • written 10 months ago by • 0
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0
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373
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DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
11 months ago jean-christophe.helbling • 0
2
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4
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837
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
13 months ago • updated 12 months ago thomas.heigl.ibk • 0
0
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2
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661
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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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704
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
16 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 18 months ago by ★ 1.9k • written 18 months ago by • 0
0
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3
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1.3k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 18 months ago by 16k • written 19 months ago by • 0
0
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2
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954
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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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2.5k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 20 months ago by ▴ 20 • written 2.3 years ago by ▴ 20
1
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5
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1.3k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 20 months ago by ★ 1.9k • written 20 months ago by • 0
0
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0
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660
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
21 months ago nick_brittain55 • 0
0
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0
replies
591
views
Error while performing DEXseq
DEXSeq
21 months ago vipul14 • 0
0
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0
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597
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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 `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.1 years ago Ben J ▴ 20
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0
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827
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DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.2 years ago by 43k • written 2.3 years ago by • 0
0
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1
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1.0k
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plotDEXSeq error?
DEXSeq dex
2.3 years ago barrypraveen • 0
1
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4
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1.2k
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DEXseq batch removal
DEXSeq
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by ▴ 10
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0
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576
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.5 years ago Matthias Munz ▴ 20
0
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0
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688
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.6 years ago osieman52 • 0
1
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2
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1.1k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
2.6 years ago Delta._.43 ▴ 20
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1
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1.1k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.8 years ago NIK • 0
0
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4
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2.1k
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DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.8 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 5.9 years ago by • 0
8
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12
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4.2k
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 9 months ago by ▴ 30 • written 2.9 years ago by ▴ 380
3
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2
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1.4k
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DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.9 years ago • updated 2.8 years ago Dakarai ▴ 10
1
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1
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895
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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
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1.2k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.3 years ago • updated 3.1 years ago A ▴ 40
3
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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
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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 3.1 years ago by ★ 1.9k • written 3.4 years ago by • 0
1
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1
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1.4k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3.1 years ago by ★ 1.9k • written 3.5 years ago by ▴ 10
2
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7
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1.7k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.5 years ago rbenel ▴ 40
0
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5
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1.6k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.6 years ago • updated 3.5 years ago bioinformatic_trainee ▴ 10
1
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0
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1.4k
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.6 years ago Matthias Munz ▴ 20
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0
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851
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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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832
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DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.7 years ago Matthias Munz ▴ 20
1
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6
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2.0k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.7 years ago by ▴ 120 • written 3.9 years ago by ▴ 10
4
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5
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2.5k
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
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Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.9 years ago jbono ▴ 10
0
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2
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1.3k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.9 years ago Gaia • 0
3
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2
replies
1.3k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
4.0 years ago Angel ▴ 10
2
votes
2
replies
1.5k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.0 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 4.2 years ago by ★ 1.9k • written 4.2 years ago by • 0
0
votes
2
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1.6k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
4.7 years ago • updated 4.3 years ago aleksandar.baburski.g • 0
50 results • Page 1 of 1
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Answer: pairedGSEA input files by James W. MacDonald 68k
If you want to do a splicing analysis, you cannot have counts/gene because the counts are aggregated at the gene level, not the transcript …
Answer: Group-specific condition effects with individuals nested: matrix is not full ra by James W. MacDonald 68k
Yes to both questions.
Answer: TheProcess got Killed by James W. MacDonald 68k
'The process got killed' doesn't provide much information. That could be due to more than one thing. But the simplest explanation is that y…
Answer: Vertical line at A=0, nothing else, on MA plot by melissa • 0
Thank you so much @mikelove ! I was searching for a solution for hours. You made a PhD student very happy. Greetings
Comment: Group-specific condition effects with individuals nested: matrix is not full ra by picasa1983 • 0
Sorry I made a typo in my table (now edited). The donor 4 actually has the 2 conditions: KO and WT. I think I found the issue: my design m…
Votes
C: Vertical line at A=0, nothing else, on MA plot
Answer: SingleCellExperiment convenience function for metadata+expression?
Answer: SingleCellExperiment convenience function for metadata+expression?
Answer: help documentation for keytypes in annotationdbi packages
Interpreting DESEQ2 interaction term and inclusion of covariate
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