Showing : DEXseq • reset
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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 • 0 • written 9.4 years ago by ▴ 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
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2
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1.4k
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JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq splicing RNAseq DEXSeq
written 6.3 years ago by ▴ 10
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1
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380
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Make DEXSeq plot normal scale
DEXSeq Dexseq
updated 10 months ago by 68k • written 10 months ago by • 0
4
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6
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1.8k
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 11 months ago by ★ 5.0k • written 12 months ago by • 0
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0
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445
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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
13 months ago cftattersfield • 0
0
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1
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626
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
2
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1
reply
902
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How to design DEXSeq formula for multiple variables
DEXSeq
22 months ago • updated 21 months ago Sara • 0
8
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12
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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 ▴ 30 • written 3.9 years ago by ▴ 390
3
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1
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1.0k
views
How to save the DEXSeq results
DEXSeq
updated 22 months ago by 43k • written 22 months ago by • 0
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3
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972
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 22 months ago by ★ 1.9k • written 23 months ago by • 0
0
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0
replies
618
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
22 months ago Sara • 0
0
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1
reply
780
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Adding columns to DEXSeqResults object
DEXSeq
updated 23 months ago by ★ 1.9k • written 23 months ago by • 0
0
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1
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1.8k
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 23 months ago by 43k • written 23 months ago by • 0
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0
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559
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DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
2.0 years ago jean-christophe.helbling • 0
2
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4
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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
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2
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911
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Swimming downstream: transcript fold changes
DEXSeq stageR
2.3 years ago jbono ▴ 10
1
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1
reply
1.0k
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
2.4 years ago NiKo ▴ 10
0
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2
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1.4k
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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
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3
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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 ★ 1.9k • written 2.5 years ago by • 0
0
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3
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1.9k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
8
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7
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3.3k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 2.7 years ago by ▴ 20 • written 3.4 years ago by ▴ 20
1
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5
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1.7k
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DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 2.7 years ago by ★ 1.9k • written 2.7 years ago by • 0
0
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0
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893
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
2.8 years ago nick_brittain55 • 0
0
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0
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777
views
Error while performing DEXseq
DEXSeq
2.8 years ago vipul14 • 0
0
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0
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827
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
3.0 years ago Ben J ▴ 20
2
votes
2
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2.0k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
3.1 years ago Ben J ▴ 20
1
vote
15
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4.7k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 3.2 years ago by • 0 • written 8.9 years ago by • 0
0
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0
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1.1k
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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1
reply
1.3k
views
plotDEXSeq error?
DEXSeq dex
3.3 years ago barrypraveen • 0
1
vote
4
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1.6k
views
DEXseq batch removal
DEXSeq
updated 3.4 years ago by ★ 1.9k • written 3.4 years ago by ▴ 10
0
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0
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800
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
3.5 years ago Matthias Munz ▴ 20
1
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2
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2.6k
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DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 3.6 years ago by ▴ 10 • written 6.6 years ago by ▴ 10
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0
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887
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.6 years ago osieman52 • 0
1
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2
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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
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1
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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
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4
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2.8k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 3.8 years ago by ▴ 100 • written 3.9 years ago by • 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
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5
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2.7k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 6.9 years ago by • 0
1
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1
reply
1.1k
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 4.0 years ago by ★ 1.9k • written 4.0 years ago by • 0
1
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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
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1
reply
1.8k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 4.1 years ago by ★ 1.9k • written 4.5 years ago by ▴ 10
0
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1
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1.4k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 4.1 years ago by ★ 1.9k • written 4.4 years ago by • 0
3
votes
3
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1.8k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 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 • 0 • written 9.1 years ago by ★ 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
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2.8k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 4.5 years ago by ▴ 20 • written 5.9 years ago by ▴ 20
0
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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 1 of 8
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Comment: Quick two questions on limpa by J Kim • 0
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 by Michael Love 43k
You could try `glmGamPoi` fitting via `fitType`: https://github.com/thelovelab/DESeq2/blob/devel/man/DESeq.Rd#L10 This is a more rece…
Answer: Limma-voom sample weights and impact on DEG numbers by Taimor • 0
<a href="https://tntsimregisteer.com/">talk n text sim registration</a> officially provides three safe and authorized ways to register sim…
Answer: Quick two questions on limpa by Gordon Smyth 53k
Thanks for your questions about limpa. The short answer is that you should use the default settings of the readSpectronaut() function. The…
Comment: ComplexHeatmap removes row labels if annotation is added by RosaliaSchulist99 • 0
thanks for sharing https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#automatic-adjustment-to-the-main-heatmap
Votes
Answer: Quick two questions on limpa
Answer: Quick two questions on limpa
Comment: tximeta cannot open annotation gtf?
Answer: tximeta cannot open annotation gtf?
Comment: Question about using LRT test for time course experiments with DESeq2
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