Showing : DEXSEq • reset
4
votes
5
replies
940
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 7 days ago by • 0 • written 20 days ago by • 0
0
votes
0
replies
109
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
8 weeks ago cftattersfield • 0
0
votes
1
reply
401
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 8 months ago by ★ 4.8k • written 8 months ago by • 0
2
votes
1
reply
573
views
How to design DEXSeq formula for multiple variables
DEXSeq
10 months ago • updated 9 months ago Sara • 0
3
votes
1
reply
655
views
How to save the DEXSeq results
DEXSeq
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
0
replies
345
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
11 months ago Sara • 0
0
votes
3
replies
602
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 11 months ago by ★ 1.9k • written 11 months ago by • 0
0
votes
1
reply
465
views
Adding columns to DEXSeqResults object
DEXSeq
updated 11 months ago by ★ 1.9k • written 11 months ago by • 0
0
votes
1
reply
892
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
0
replies
384
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
12 months ago jean-christophe.helbling • 0
2
votes
4
replies
870
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
13 months ago thomas.heigl.ibk • 0
0
votes
2
replies
686
views
Swimming downstream: transcript fold changes
DEXSeq stageR
16 months ago jbono ▴ 10
1
vote
1
reply
732
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
17 months ago NiKo ▴ 10
0
votes
3
replies
1.1k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 19 months ago by ★ 1.9k • written 19 months ago by • 0
0
votes
3
replies
1.4k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 19 months ago by 16k • written 20 months ago by • 0
0
votes
2
replies
988
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
19 months ago • updated 18 months ago yr542 • 0
8
votes
7
replies
2.6k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 21 months ago by ▴ 20 • written 2.4 years ago by ▴ 20
1
vote
5
replies
1.3k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 21 months ago by ★ 1.9k • written 21 months ago by • 0
0
votes
0
replies
676
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
21 months ago nick_brittain55 • 0
0
votes
0
replies
610
views
Error while performing DEXseq
DEXSeq
22 months ago vipul14 • 0
0
votes
0
replies
608
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
2.0 years ago Ben J ▴ 20
2
votes
2
replies
1.6k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.1 years ago Ben J ▴ 20
0
votes
0
replies
845
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
1
reply
1.1k
views
plotDEXSeq error?
DEXSeq dex
2.4 years ago • updated 2.3 years ago barrypraveen • 0
1
vote
4
replies
1.3k
views
DEXseq batch removal
DEXSeq
updated 2.5 years ago by ★ 1.9k • written 2.5 years ago by ▴ 10
0
votes
0
replies
589
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.6 years ago Matthias Munz ▴ 20
0
votes
0
replies
704
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.6 years ago osieman52 • 0
1
vote
2
replies
1.2k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
2.6 years ago Delta._.43 ▴ 20
0
votes
1
reply
1.2k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.8 years ago NIK • 0
0
votes
4
replies
2.2k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.8 years ago by ▴ 90 • written 2.9 years ago by • 0
0
votes
5
replies
2.4k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 6.0 years ago by • 0
8
votes
12
replies
4.3k
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 10 months ago by ▴ 30 • written 2.9 years ago by ▴ 380
3
votes
2
replies
1.5k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.0 years ago • updated 2.9 years ago Dakarai ▴ 10
1
vote
1
reply
919
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 3.0 years ago by ★ 1.9k • written 3.0 years ago by • 0
1
vote
2
replies
1.3k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.3 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 3.2 years ago by 43k • written 3.2 years ago by ▴ 120
0
votes
1
reply
1.1k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 3.2 years ago by ★ 1.9k • written 3.4 years ago by • 0
1
vote
1
reply
1.5k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3.2 years ago by ★ 1.9k • written 3.6 years ago by ▴ 10
2
votes
7
replies
1.7k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.6 years ago rbenel ▴ 40
0
votes
5
replies
1.7k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.6 years ago bioinformatic_trainee ▴ 10
1
vote
0
replies
1.4k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.7 years ago Matthias Munz ▴ 20
0
votes
0
replies
866
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.7 years ago n.tear ▴ 20
0
votes
0
replies
851
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.8 years ago Matthias Munz ▴ 20
1
vote
6
replies
2.0k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.8 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
3.9 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.1k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
4.0 years ago jbono ▴ 10
0
votes
2
replies
1.3k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
4.0 years ago Gaia • 0
3
votes
2
replies
1.4k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
4.1 years ago • updated 4.0 years ago Angel ▴ 10
2
votes
2
replies
1.5k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.1 years ago • updated 4.0 years ago n.tear ▴ 20
1
vote
1
reply
1.3k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 4.2 years ago by ★ 1.9k • written 4.2 years ago by • 0
50 results • Page 1 of 1
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Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
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Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
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