Showing : dexseq • reset
2
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74
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How to design DEXSeq formula for multiple variables
DEXSeq
updated 4 days ago by ★ 1.9k • written 6 days ago by • 0
3
votes
1
reply
150
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How to save the DEXSeq results
DEXSeq
updated 13 days ago by 42k • written 13 days ago by • 0
0
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0
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99
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
25 days ago • updated 20 days ago Sara • 0
0
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3
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189
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 19 days ago by ★ 1.9k • written 4 weeks ago by • 0
0
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1
reply
167
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Adding columns to DEXSeqResults object
DEXSeq
updated 4 weeks ago by ★ 1.9k • written 4 weeks ago by • 0
0
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1
reply
128
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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0
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145
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
9 weeks ago jean-christophe.helbling • 0
2
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4
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449
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
3 months ago • updated 11 weeks ago thomas.heigl.ibk • 0
0
votes
2
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397
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Swimming downstream: transcript fold changes
DEXSeq stageR
6 months ago jbono ▴ 10
1
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1
reply
417
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
6 months ago NiKo ▴ 10
0
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3
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693
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 8 months ago by ★ 1.9k • written 8 months ago by • 0
0
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3
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809
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Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 9 months ago by 16k • written 10 months ago by • 0
0
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2
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584
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
9 months ago • updated 8 months ago yr542 • 0
8
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7
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1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 19 months ago by ▴ 20
1
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5
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883
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
0
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0
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400
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
11 months ago nick_brittain55 • 0
0
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0
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410
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Error while performing DEXseq
DEXSeq
11 months ago vipul14 • 0
0
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0
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435
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
14 months ago Ben J • 0
0
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2
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923
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
15 months ago Ben J • 0
0
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0
replies
589
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 17 months ago by 42k • written 17 months ago by • 0
0
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1
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819
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plotDEXSeq error?
DEXSeq dex
18 months ago barrypraveen • 0
1
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4
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961
views
DEXseq batch removal
DEXSeq
updated 19 months ago by ★ 1.9k • written 19 months ago by ▴ 10
0
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0
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431
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
20 months ago Matthias Munz ▴ 10
0
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0
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517
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
21 months ago osieman52 • 0
1
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2
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844
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
21 months ago Delta._.43 ▴ 20
0
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1
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869
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DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
24 months ago NIK • 0
0
votes
4
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1.5k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 24 months ago by ▴ 90 • written 2.0 years ago by • 0
0
votes
5
replies
2.0k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.1 years ago by • 0
6
votes
11
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3.1k
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 14 months ago by • 0 • written 2.1 years ago by ▴ 360
3
votes
2
replies
969
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.1 years ago • updated 2.0 years ago Dakarai ▴ 10
1
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1
reply
665
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.2 years ago by ★ 1.9k • written 2.2 years ago by • 0
1
vote
2
replies
885
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.5 years ago • updated 2.3 years ago A ▴ 40
3
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3
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1.1k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.3 years ago by 42k • written 2.4 years ago by ▴ 120
0
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1
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861
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.3 years ago by ★ 1.9k • written 2.6 years ago by • 0
1
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1
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1.1k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.3 years ago by ★ 1.9k • written 2.7 years ago by ▴ 10
2
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7
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1.3k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
2.7 years ago rbenel ▴ 40
0
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5
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1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.8 years ago bioinformatic_trainee ▴ 10
0
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0
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845
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.8 years ago Matthias Munz ▴ 10
0
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0
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647
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
2.9 years ago n.tear ▴ 20
0
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0
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650
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DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.9 years ago Matthias Munz ▴ 10
1
vote
6
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1.6k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 2.9 years ago by ▴ 120 • written 3.1 years ago by ▴ 10
4
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5
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1.9k
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
3.1 years ago • updated 3.0 years ago Matthias Munz ▴ 10
0
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0
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887
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.1 years ago jbono ▴ 10
0
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2
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1.0k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.2 years ago Gaia • 0
3
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2
replies
1.1k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.2 years ago Angel ▴ 10
2
votes
2
replies
1.2k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.3 years ago • updated 3.2 years ago n.tear ▴ 20
1
vote
1
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1.0k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3.4 years ago by ★ 1.9k • written 3.4 years ago by • 0
0
votes
2
replies
1.3k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
3.9 years ago • updated 3.5 years ago aleksandar.baburski.g • 0
1
vote
6
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4.0k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.5 years ago by ▴ 20 • written 9.2 years ago by • 0
0
votes
2
replies
1.5k
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 3.5 years ago by ▴ 20 • written 6.4 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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