Showing : DEXseq • reset
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78
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Make DEXSeq plot normal scale
DEXSeq Dexseq
updated 3 days ago by 68k • written 4 days ago by • 0
4
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6
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1.2k
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 28 days ago by ★ 4.8k • written 7 weeks ago by • 0
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0
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144
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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
12 weeks ago cftattersfield • 0
0
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1
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433
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 9 months ago by ★ 4.8k • written 9 months ago by • 0
2
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1
reply
615
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How to design DEXSeq formula for multiple variables
DEXSeq
11 months ago • updated 10 months ago Sara • 0
3
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1
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711
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How to save the DEXSeq results
DEXSeq
updated 11 months ago by 43k • written 11 months ago by • 0
0
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0
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368
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
12 months ago Sara • 0
0
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3
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641
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 12 months ago by ★ 1.9k • written 12 months ago by • 0
0
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1
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492
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Adding columns to DEXSeqResults object
DEXSeq
updated 12 months ago by ★ 1.9k • written 12 months ago by • 0
0
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1
reply
989
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 12 months ago by 43k • written 12 months ago by • 0
0
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0
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403
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
13 months ago jean-christophe.helbling • 0
2
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4
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900
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
14 months ago thomas.heigl.ibk • 0
0
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2
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707
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Swimming downstream: transcript fold changes
DEXSeq stageR
17 months ago jbono ▴ 10
1
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1
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769
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
18 months ago NiKo ▴ 10
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3
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1.1k
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 20 months ago by ★ 1.9k • written 20 months ago by • 0
0
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3
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1.4k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 20 months ago by 16k • written 21 months ago by • 0
0
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2
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1.0k
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DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
20 months ago • updated 19 months ago yr542 • 0
8
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7
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2.6k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 22 months ago by ▴ 20 • written 2.5 years ago by ▴ 20
1
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5
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1.3k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 22 months ago by ★ 1.9k • written 22 months ago by • 0
0
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0
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694
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
22 months ago nick_brittain55 • 0
0
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0
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629
views
Error while performing DEXseq
DEXSeq
23 months ago vipul14 • 0
0
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0
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627
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
2.1 years ago Ben J ▴ 20
2
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2
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1.6k
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.2 years ago Ben J ▴ 20
0
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0
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875
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DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
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1
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1.1k
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plotDEXSeq error?
DEXSeq dex
2.4 years ago barrypraveen • 0
1
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4
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1.3k
views
DEXseq batch removal
DEXSeq
updated 2.5 years ago by ★ 1.9k • written 2.5 years ago by ▴ 10
0
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0
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607
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.6 years ago Matthias Munz ▴ 20
0
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0
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725
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.7 years ago osieman52 • 0
1
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2
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1.2k
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DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
2.7 years ago Delta._.43 ▴ 20
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1
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1.2k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.9 years ago NIK • 0
0
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4
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2.2k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.9 years ago by ▴ 90 • written 3.0 years ago by • 0
0
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5
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2.4k
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DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 6.0 years ago by • 0
8
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12
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4.4k
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 11 months ago by ▴ 30 • written 3.0 years ago by ▴ 380
3
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2
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1.5k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.1 years ago • updated 3.0 years ago Dakarai ▴ 10
1
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1
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938
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 3.1 years ago by ★ 1.9k • written 3.1 years ago by • 0
1
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2
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1.3k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.4 years ago • updated 3.2 years ago A ▴ 60
3
votes
3
replies
1.5k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.3 years ago by 43k • written 3.3 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 3.3 years ago by ★ 1.9k • written 3.5 years ago by • 0
1
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1
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1.5k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3.3 years ago by ★ 1.9k • written 3.7 years ago by ▴ 10
2
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7
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1.8k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.7 years ago • updated 3.6 years ago rbenel ▴ 40
0
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5
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1.7k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.7 years ago bioinformatic_trainee ▴ 10
1
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0
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1.4k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.8 years ago Matthias Munz ▴ 20
0
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0
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882
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.8 years ago n.tear ▴ 20
0
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0
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867
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.8 years ago Matthias Munz ▴ 20
1
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6
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2.1k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.9 years ago by ▴ 120 • written 4.0 years ago by ▴ 10
4
votes
5
replies
2.6k
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
4.0 years ago Matthias Munz ▴ 20
0
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0
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1.2k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
4.1 years ago jbono ▴ 10
0
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2
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1.4k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
4.1 years ago Gaia • 0
3
votes
2
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1.4k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
4.1 years ago Angel ▴ 10
2
votes
2
replies
1.5k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.2 years ago • updated 4.1 years ago n.tear ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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