Showing : DEXseq • reset
4
votes
6
replies
1.2k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 14 days ago by ★ 4.8k • written 5 weeks ago by • 0
0
votes
0
replies
125
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
10 weeks ago cftattersfield • 0
0
votes
1
reply
418
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
595
views
How to design DEXSeq formula for multiple variables
DEXSeq
11 months ago • updated 10 months ago Sara • 0
3
votes
1
reply
686
views
How to save the DEXSeq results
DEXSeq
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
0
replies
356
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
11 months ago Sara • 0
0
votes
3
replies
625
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
475
views
Adding columns to DEXSeqResults object
DEXSeq
updated 11 months ago by ★ 1.9k • written 12 months ago by • 0
0
votes
1
reply
946
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
395
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
13 months ago jean-christophe.helbling • 0
2
votes
4
replies
885
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
14 months ago • updated 13 months ago thomas.heigl.ibk • 0
0
votes
2
replies
694
views
Swimming downstream: transcript fold changes
DEXSeq stageR
17 months ago jbono ▴ 10
1
vote
1
reply
754
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 20 months ago by 16k • written 20 months ago by • 0
0
votes
2
replies
1000
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
20 months ago • updated 19 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 2.5 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
687
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
22 months ago nick_brittain55 • 0
0
votes
0
replies
619
views
Error while performing DEXseq
DEXSeq
22 months ago vipul14 • 0
0
votes
0
replies
615
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
2.1 years ago Ben J ▴ 20
2
votes
2
replies
1.6k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.2 years ago Ben J ▴ 20
0
votes
0
replies
860
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
votes
1
reply
1.1k
views
plotDEXSeq error?
DEXSeq dex
2.4 years ago barrypraveen • 0
1
vote
4
replies
1.3k
views
DEXseq batch removal
DEXSeq
updated 2.5 years ago by ★ 1.9k • written 2.5 years ago by ▴ 10
0
votes
0
replies
595
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.6 years ago Matthias Munz ▴ 20
0
votes
0
replies
711
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.7 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
2.7 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
2.9 years ago NIK • 0
0
votes
4
replies
2.2k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.9 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 3.0 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
927
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
vote
2
replies
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 3.2 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 3.5 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
1.8k
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
3.7 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
871
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
855
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
4.0 years ago • updated 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
4.1 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 Angel ▴ 10
2
votes
2
replies
1.5k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.1 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 4.3 years ago by ★ 1.9k • written 4.3 years ago by • 0
50 results • Page 1 of 1
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> I would like to ask whether it would make sense to first normalize the count data using DESeq2 and VST before performing WGCNA. This …
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Hi, sorry for the delay in getting back to you, probably by now you found the solution yourself, but just in case you didn't or anybody els…
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In general, using the entire dataset and then just comparing the subgroups you want within the whole dataset is preferable.
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If these are two different batches then they're fully confounded making it statistically invalid. Biologically, I find it at least question…
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Hi, please consider asking this at biostars.org as here we're mainly answering precise technical questions towards the packages. You are se…
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