Showing : DEXseq • reset
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332
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 5 months ago by ★ 4.6k • written 5 months ago by • 0
2
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1
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442
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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
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518
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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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300
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
8 months ago Sara • 0
0
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3
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520
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 8 months ago by ★ 1.9k • written 9 months ago by • 0
0
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1
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403
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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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644
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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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348
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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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782
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
11 months ago • updated 10 months ago thomas.heigl.ibk • 0
0
votes
2
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623
views
Swimming downstream: transcript fold changes
DEXSeq stageR
14 months ago jbono ▴ 10
1
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1
reply
668
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
14 months ago NiKo ▴ 10
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3
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997
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 16 months ago by ★ 1.9k • written 16 months ago by • 0
0
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3
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1.3k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 17 months ago by 16k • written 17 months ago by • 0
0
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2
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880
views
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
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 18 months ago by ▴ 20 • written 2.2 years ago by ▴ 20
1
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5
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1.2k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 18 months ago by ★ 1.9k • written 18 months ago by • 0
0
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0
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628
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
19 months ago nick_brittain55 • 0
0
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0
replies
568
views
Error while performing DEXseq
DEXSeq
19 months ago vipul14 • 0
0
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0
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569
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
22 months ago Ben J ▴ 20
2
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2
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1.4k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
23 months ago Ben J ▴ 20
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0
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793
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DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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1
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1.0k
views
plotDEXSeq error?
DEXSeq dex
2.2 years ago • updated 2.1 years ago barrypraveen • 0
1
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4
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1.2k
views
DEXseq batch removal
DEXSeq
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by ▴ 10
0
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0
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546
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.4 years ago Matthias Munz ▴ 20
0
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0
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664
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.4 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
2.4 years ago Delta._.43 ▴ 20
0
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1
reply
1.1k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.6 years ago NIK • 0
0
votes
4
replies
2.0k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.6 years ago by ▴ 90 • written 2.7 years ago by • 0
0
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5
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2.3k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.8 years ago by • 0
8
votes
12
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4.0k
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 7 months ago by ▴ 30 • written 2.7 years ago by ▴ 380
3
votes
2
replies
1.3k
views
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
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1
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866
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.8 years ago by ★ 1.9k • written 2.8 years ago by • 0
1
vote
2
replies
1.2k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.1 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
reply
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 3.2 years ago by • 0
1
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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
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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
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.4 years ago bioinformatic_trainee ▴ 10
1
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0
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1.3k
views
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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818
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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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795
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.6 years ago Matthias Munz ▴ 20
1
vote
6
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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
3.7 years ago Matthias Munz ▴ 20
0
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0
replies
1.1k
views
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
3.8 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 • updated 3.8 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 • updated 3.8 years ago n.tear ▴ 20
1
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1
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1.2k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 4.0 years ago by ★ 1.9k • written 4.0 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
1
vote
6
replies
4.5k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 4.2 years ago by ▴ 20 • written 9.8 years ago by • 0
50 results • Page 1 of 1
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Replies
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
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