Showing : Dexseq • reset
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15
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Differential splicing from SGSeq analysis
DEXSeq SGSeq
20 hours ago • updated 19 hours ago Sara • 0
0
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1
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82
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 days ago by ★ 1.9k • written 6 days ago by • 0
0
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1
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116
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Adding columns to DEXSeqResults object
DEXSeq
updated 6 days ago by ★ 1.9k • written 8 days ago by • 0
0
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1
reply
86
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 6 days ago by 41k • written 7 days ago by • 0
0
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0
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125
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DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
6 weeks ago jean-christophe.helbling • 0
2
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4
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394
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
11 weeks ago • updated 8 weeks ago thomas.heigl.ibk • 0
0
votes
2
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348
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Swimming downstream: transcript fold changes
DEXSeq stageR
5 months ago jbono ▴ 10
1
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1
reply
369
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
5 months ago NiKo ▴ 10
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3
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639
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 7 months ago by ★ 1.9k • written 7 months ago by • 0
0
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3
replies
755
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 8 months ago by 16k • written 9 months ago by • 0
0
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2
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543
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DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
8 months ago • updated 7 months ago yr542 • 0
8
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7
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1.7k
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Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 9 months ago by ▴ 20 • written 18 months ago by ▴ 20
1
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5
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828
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 9 months ago by ★ 1.9k • written 9 months ago by • 0
0
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0
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371
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
10 months ago nick_brittain55 • 0
0
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0
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384
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Error while performing DEXseq
DEXSeq
11 months ago vipul14 • 0
0
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0
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413
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
13 months ago Ben J • 0
0
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2
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880
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
14 months ago Ben J • 0
0
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0
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563
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 17 months ago by 41k • written 17 months ago by • 0
0
votes
1
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784
views
plotDEXSeq error?
DEXSeq dex
17 months ago barrypraveen • 0
1
vote
4
replies
905
views
DEXseq batch removal
DEXSeq
updated 18 months ago by ★ 1.9k • written 18 months ago by ▴ 10
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0
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409
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
19 months ago Matthias Munz ▴ 10
0
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0
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488
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
20 months ago osieman52 • 0
1
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2
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810
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DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
20 months ago Delta._.43 ▴ 20
0
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1
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823
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DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
23 months ago NIK • 0
0
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4
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1.4k
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DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 23 months ago by ▴ 90 • written 24 months ago by • 0
0
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5
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1.9k
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DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.0 years ago by • 0
6
votes
11
replies
3.0k
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 13 months ago by • 0 • written 2.0 years ago by ▴ 350
3
votes
2
replies
930
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.1 years ago • updated 24 months ago Dakarai ▴ 10
1
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1
reply
635
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.1 years ago by ★ 1.9k • written 2.1 years ago by • 0
1
vote
2
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852
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Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.4 years ago • updated 2.2 years ago A ▴ 40
3
votes
3
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1.1k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.3 years ago by 41k • written 2.3 years ago by ▴ 120
0
votes
1
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831
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.3 years ago by ★ 1.9k • written 2.5 years ago by • 0
1
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1
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1.1k
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DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.3 years ago by ★ 1.9k • written 2.7 years ago by ▴ 10
2
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7
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1.2k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
2.7 years ago • updated 2.6 years ago rbenel ▴ 40
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5
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1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.7 years ago bioinformatic_trainee ▴ 10
0
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0
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811
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.7 years ago Matthias Munz ▴ 10
0
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0
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625
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
2.8 years ago n.tear ▴ 20
0
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0
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625
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.8 years ago Matthias Munz ▴ 10
1
vote
6
replies
1.5k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 2.9 years ago by ▴ 120 • written 3.0 years ago by ▴ 10
4
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5
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1.9k
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DEXSeq: What's the best way to map an exon counting bin, e.g. E002 to exon(s) or position in transcript(s)
DEXSeq
3.0 years ago Matthias Munz ▴ 10
0
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0
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860
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.1 years ago jbono ▴ 10
0
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2
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985
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.1 years ago Gaia • 0
3
votes
2
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1.0k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.1 years ago Angel ▴ 10
2
votes
2
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1.2k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.2 years ago • updated 3.1 years ago n.tear ▴ 20
1
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1
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973
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3.3 years ago by ★ 1.9k • written 3.3 years ago by • 0
0
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2
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1.2k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
3.8 years ago • updated 3.4 years ago aleksandar.baburski.g • 0
1
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6
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3.9k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.4 years ago by ▴ 20 • written 9.1 years ago by • 0
0
votes
2
replies
1.5k
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Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 3.4 years ago by ▴ 20 • written 6.3 years ago by • 0
6
votes
7
replies
1.7k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 3.3 years ago by 41k • written 3.5 years ago by ▴ 20
0
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2
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868
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 3.8 years ago by ★ 3.7k • written 3.8 years ago by • 0
50 results • Page 1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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