Showing : DEXseq • reset
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101
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Testing subgroup-specific interactions in DEXSeq
DEXSeq RNASeqData Transcriptomics
23 days ago • updated 19 days ago palanikumars2 • 0
0
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1
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378
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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
0
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0
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439
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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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625
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
2
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1
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901
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How to design DEXSeq formula for multiple variables
DEXSeq
22 months ago • updated 21 months ago Sara • 0
3
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1
reply
1.0k
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How to save the DEXSeq results
DEXSeq
updated 22 months ago by 43k • written 22 months ago by • 0
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0
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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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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 22 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 22 months ago by 43k • written 22 months ago by • 0
0
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1
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775
views
Adding columns to DEXSeqResults object
DEXSeq
updated 22 months ago by ★ 1.9k • 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
24 months ago jean-christophe.helbling • 0
2
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4
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1.3k
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
2.1 years ago • updated 2.0 years ago thomas.heigl.ibk • 0
0
votes
2
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909
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Swimming downstream: transcript fold changes
DEXSeq stageR
2.3 years ago jbono ▴ 10
1
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1
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1.0k
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
2.4 years ago NiKo ▴ 10
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3
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1.5k
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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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2
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1.4k
views
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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1.9k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
1
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5
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1.7k
views
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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892
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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776
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Error while performing DEXseq
DEXSeq
2.8 years ago vipul14 • 0
0
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0
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825
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
3.0 years ago Ben J ▴ 20
2
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2
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2.0k
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
3.1 years ago Ben J ▴ 20
0
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0
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1.1k
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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1
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1.3k
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plotDEXSeq error?
DEXSeq dex
3.3 years ago barrypraveen • 0
8
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7
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3.3k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 2.7 years ago by ▴ 20 • written 3.4 years ago by ▴ 20
1
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4
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1.6k
views
DEXseq batch removal
DEXSeq
updated 3.4 years ago by ★ 1.9k • written 3.4 years ago by ▴ 10
0
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0
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798
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
3.5 years ago Matthias Munz ▴ 20
0
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0
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887
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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
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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
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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
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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2
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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 • updated 3.8 years ago Dakarai ▴ 10
1
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1
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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
3
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3
replies
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
1
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2
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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
0
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1
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1.4k
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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
1
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1
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1.8k
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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
2
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7
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2.2k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
4.5 years ago rbenel ▴ 50
0
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5
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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
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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
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0
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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
0
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0
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1.1k
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
4.7 years ago Matthias Munz ▴ 20
4
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5
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3.1k
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
4.9 years ago • updated 4.8 years ago Matthias Munz ▴ 20
1
vote
6
replies
2.7k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 4.7 years ago by ▴ 120 • written 4.9 years ago by ▴ 10
0
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0
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1.4k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
4.9 years ago jbono ▴ 10
0
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2
replies
1.7k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
5.0 years ago Gaia • 0
3
votes
2
replies
1.7k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
5.0 years ago Angel ▴ 10
2
votes
2
replies
1.9k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
5.1 years ago • updated 5.0 years ago n.tear ▴ 20
364 results • Page 1 of 8
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Comment: Inclusion of non-coding portions of transcripts (UTR-regions and introns) within by Pat • 0
Ill be honest, I didnt trust any of these services for a long time. Im a political science major and the pressure around writing is intense…
Comment: Question on processing compound protein groups in limpa by brianpeterson1210 • 0
Thank you[,][1] Appreciated! [1]: http://paint3d.org
Comment: Subsetting DDS object for individual conditions over time by A ▴ 60
Hi @atpoint Thank you for the quick reply! and this makes sense! I will confirm with a corr to see how the SFs differ but also how DE dif…
Answer: Subsetting DDS object for individual conditions over time by ATpoint ★ 5.0k
It would surprise my quite a bit if the size factors would differ notably between subset or not. I would always try to keep the size factor…
Comment: GSEA error by Adithi • 0
Thank you so much. That makes perfect sense to me. I will work on this.
Votes
Comment: Question about using LRT test for time course experiments with DESeq2
A: DESeq2 LRT test for multi-factor designs
Answer: RNA Seq using Lrt
Answer: DESeq2 LRT Reduced Formula
Answer: DESeq2: LRT or WALD guidance
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