Showing : DEXseq • reset
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Testing subgroup-specific interactions in DEXSeq
DEXSeq RNASeqData Transcriptomics
18 days ago • updated 14 days ago palanikumars2 • 0
0
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1
reply
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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434
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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
reply
624
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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
reply
900
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How to design DEXSeq formula for multiple variables
DEXSeq
21 months ago • updated 20 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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615
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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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969
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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
reply
774
views
Adding columns to DEXSeqResults object
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
views
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
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0
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558
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
24 months ago jean-christophe.helbling • 0
2
votes
4
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1.3k
views
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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908
views
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
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
2.3 years ago NiKo ▴ 10
0
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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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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
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
8
votes
7
replies
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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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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890
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
2.7 years ago nick_brittain55 • 0
0
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0
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775
views
Error while performing DEXseq
DEXSeq
2.8 years ago vipul14 • 0
0
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0
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822
views
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
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
3.1 years ago Ben J ▴ 20
0
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0
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1.1k
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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1
reply
1.3k
views
plotDEXSeq error?
DEXSeq dex
3.3 years ago barrypraveen • 0
1
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4
replies
1.6k
views
DEXseq batch removal
DEXSeq
updated 3.4 years ago by ★ 1.9k • written 3.4 years ago by ▴ 10
0
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0
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792
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
3.5 years ago Matthias Munz ▴ 20
0
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0
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886
views
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
views
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
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 3.8 years ago by ▴ 100 • written 3.8 years ago by • 0
0
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5
replies
2.7k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 6.9 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
replies
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 3.9 years ago by ★ 1.9k • written 4.0 years ago by • 0
1
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2
replies
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
3
votes
3
replies
1.8k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 120
0
votes
1
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1.4k
views
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
views
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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2.1k
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
4.6 years ago n.tear ▴ 20
0
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0
replies
1.1k
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
4.7 years ago Matthias Munz ▴ 20
1
vote
6
replies
2.6k
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
4
votes
5
replies
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
4.8 years ago Matthias Munz ▴ 20
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
364 results • Page 1 of 8
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Answer: tximeta cannot open annotation gtf? by ATpoint ★ 5.0k
> Timeout of 60 seconds was reached You have to increase the default timeout limits for downloads, `options(timeout=3600)`. GENCODE serve…
Answer: GSEA error by James W. MacDonald 68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Answer: Unable to find ENTREZ IDs by James W. MacDonald 68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
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Answer: GSEA error
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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