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
7 hours ago cftattersfield • 0
0
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1
reply
345
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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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459
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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
543
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How to save the DEXSeq results
DEXSeq
updated 8 months ago by 43k • written 8 months ago by • 0
0
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0
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307
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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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536
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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
414
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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
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682
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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
0
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0
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358
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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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796
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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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635
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Swimming downstream: transcript fold changes
DEXSeq stageR
14 months ago jbono ▴ 10
1
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1
reply
680
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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
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1.3k
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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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905
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DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
17 months ago • updated 16 months ago yr542 • 0
8
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7
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2.4k
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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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644
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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
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576
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Error while performing DEXseq
DEXSeq
20 months ago vipul14 • 0
0
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0
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576
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
22 months ago Ben J ▴ 20
2
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2
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1.5k
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
24 months ago Ben J ▴ 20
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0
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805
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DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
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1
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1.0k
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plotDEXSeq error?
DEXSeq dex
2.2 years ago barrypraveen • 0
1
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4
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1.2k
views
DEXseq batch removal
DEXSeq
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by ▴ 10
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0
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555
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.4 years ago Matthias Munz ▴ 20
0
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0
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671
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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
views
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
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1.1k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.7 years ago NIK • 0
0
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4
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2.0k
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DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.7 years ago by ▴ 90 • written 2.7 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 • updated 2.7 years ago Dakarai ▴ 10
1
vote
1
reply
873
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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
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 3.0 years ago by 43k • written 3.0 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
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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
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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
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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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827
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.5 years ago n.tear ▴ 20
0
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0
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802
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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 • updated 3.7 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
3.8 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
replies
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
3.9 years ago n.tear ▴ 20
1
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1
reply
1.2k
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: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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A: PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
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