Showing : Dexseq • reset
0
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288
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 4 months ago by ★ 4.5k • written 4 months ago by • 0
2
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1
reply
405
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How to design DEXSeq formula for multiple variables
DEXSeq
6 months ago • updated 5 months ago Sara • 0
3
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1
reply
457
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How to save the DEXSeq results
DEXSeq
updated 6 months ago by 43k • written 6 months ago by • 0
0
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0
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278
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
7 months ago • updated 6 months ago Sara • 0
0
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3
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460
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 months ago by ★ 1.9k • written 7 months ago by • 0
0
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1
reply
365
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Adding columns to DEXSeqResults object
DEXSeq
updated 7 months ago by ★ 1.9k • written 7 months ago by • 0
0
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1
reply
546
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 7 months ago by 43k • written 7 months ago by • 0
0
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0
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322
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DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
8 months ago jean-christophe.helbling • 0
2
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4
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725
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
9 months ago thomas.heigl.ibk • 0
0
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2
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588
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Swimming downstream: transcript fold changes
DEXSeq stageR
12 months ago jbono ▴ 10
1
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1
reply
630
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
13 months ago NiKo ▴ 10
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3
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958
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 15 months ago by ★ 1.9k • written 15 months ago by • 0
0
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3
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1.2k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 15 months ago by 16k • written 16 months ago by • 0
0
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2
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843
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
15 months ago • updated 14 months ago yr542 • 0
8
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7
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2.3k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 16 months ago by ▴ 20 • written 2.1 years ago by ▴ 20
1
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5
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1.1k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 17 months ago by ★ 1.9k • written 17 months ago by • 0
0
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0
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598
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
17 months ago nick_brittain55 • 0
0
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0
replies
548
views
Error while performing DEXseq
DEXSeq
18 months ago vipul14 • 0
0
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0
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554
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
20 months ago Ben J ▴ 20
2
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2
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1.3k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
22 months ago • updated 21 months ago Ben J ▴ 20
0
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0
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761
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 24 months ago by 43k • written 24 months ago by • 0
0
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1
reply
976
views
plotDEXSeq error?
DEXSeq dex
2.0 years ago • updated 24 months ago barrypraveen • 0
1
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4
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1.1k
views
DEXseq batch removal
DEXSeq
updated 2.1 years ago by ★ 1.9k • written 2.1 years ago by ▴ 10
0
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0
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526
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.2 years ago Matthias Munz ▴ 20
0
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0
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643
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.3 years ago osieman52 • 0
1
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2
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1.0k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
2.3 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
2.5 years ago NIK • 0
0
votes
4
replies
1.9k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.5 years ago by ▴ 90 • written 2.6 years ago by • 0
0
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5
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2.2k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.6 years ago by • 0
8
votes
12
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3.9k
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 6 months ago by ▴ 30 • written 2.6 years ago by ▴ 380
3
votes
2
replies
1.2k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.6 years ago Dakarai ▴ 10
1
vote
1
reply
836
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.7 years ago by ★ 1.9k • written 2.7 years ago by • 0
1
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2
replies
1.1k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.0 years ago • updated 2.8 years ago A ▴ 40
3
votes
3
replies
1.3k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 120
0
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1
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1.0k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.8 years ago by ★ 1.9k • written 3.1 years ago by • 0
1
vote
1
reply
1.3k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.8 years ago by ★ 1.9k • written 3.3 years ago by ▴ 10
2
votes
7
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1.6k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.3 years ago • updated 3.2 years ago rbenel ▴ 40
0
votes
5
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1.5k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.3 years ago bioinformatic_trainee ▴ 10
1
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0
replies
1.2k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.3 years ago Matthias Munz ▴ 20
0
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0
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792
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.4 years ago n.tear ▴ 20
0
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0
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771
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.4 years ago Matthias Munz ▴ 20
1
vote
6
replies
1.8k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.4 years ago by ▴ 120 • written 3.6 years ago by ▴ 10
4
votes
5
replies
2.3k
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
3.6 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
3.6 years ago jbono ▴ 10
0
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2
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1.2k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.7 years ago Gaia • 0
3
votes
2
replies
1.3k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.7 years ago Angel ▴ 10
2
votes
2
replies
1.4k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.8 years ago • updated 3.7 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 3.9 years ago by ★ 1.9k • written 3.9 years ago by • 0
0
votes
2
replies
1.5k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
4.4 years ago • updated 4.0 years ago aleksandar.baburski.g • 0
1
vote
6
replies
4.4k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 4.0 years ago by ▴ 20 • written 9.7 years ago by • 0
50 results • Page 1 of 1
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Replies
Answer: Deseq2 res Function by Michael Love 43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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