Showing : dexseq • reset
2
votes
1
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56
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How to design DEXSeq formula for multiple variables
DEXSeq
updated 1 day ago by ★ 1.9k • written 3 days ago by • 0
3
votes
1
reply
142
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How to save the DEXSeq results
DEXSeq
updated 10 days ago by 42k • written 10 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
22 days ago • updated 17 days ago Sara • 0
0
votes
3
replies
184
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 16 days ago by ★ 1.9k • written 28 days ago by • 0
0
votes
1
reply
124
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 28 days ago by 42k • written 28 days ago by • 0
0
votes
1
reply
165
views
Adding columns to DEXSeqResults object
DEXSeq
updated 28 days ago by ★ 1.9k • written 4 weeks ago by • 0
0
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0
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142
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
9 weeks ago jean-christophe.helbling • 0
2
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4
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438
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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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392
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Swimming downstream: transcript fold changes
DEXSeq stageR
6 months ago jbono ▴ 10
1
vote
1
reply
410
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
6 months ago NiKo ▴ 10
0
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3
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685
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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
votes
2
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581
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
9 months ago • updated 8 months ago yr542 • 0
0
votes
3
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805
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 9 months ago by 16k • written 9 months ago by • 0
1
vote
5
replies
878
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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396
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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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408
views
Error while performing DEXseq
DEXSeq
11 months ago vipul14 • 0
0
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0
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432
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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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918
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
15 months ago Ben J • 0
0
votes
0
replies
587
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 17 months ago by 42k • written 17 months ago by • 0
0
votes
1
reply
813
views
plotDEXSeq error?
DEXSeq dex
18 months ago • updated 17 months ago barrypraveen • 0
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 19 months ago by ▴ 20
1
vote
4
replies
954
views
DEXseq batch removal
DEXSeq
updated 19 months ago by ★ 1.9k • written 19 months ago by ▴ 10
0
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0
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428
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
20 months ago Matthias Munz ▴ 10
0
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0
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513
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
21 months ago osieman52 • 0
1
vote
2
replies
841
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
votes
1
reply
862
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
24 months ago • updated 23 months ago NIK • 0
0
votes
4
replies
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
6
votes
11
replies
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
965
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
vote
1
reply
662
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.2 years ago by ★ 1.9k • written 2.2 years ago by • 0
3
votes
3
replies
1.1k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.3 years ago by 42k • written 2.3 years ago by ▴ 120
1
vote
2
replies
882
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.5 years ago • updated 2.3 years ago A ▴ 40
0
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1
reply
857
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
vote
1
reply
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
votes
7
replies
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
votes
0
replies
844
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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645
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
2.8 years ago n.tear ▴ 20
0
votes
0
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647
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.9 years ago Matthias Munz ▴ 10
4
votes
5
replies
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
3.0 years ago Matthias Munz ▴ 10
1
vote
6
replies
1.5k
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
0
votes
0
replies
884
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.1 years ago jbono ▴ 10
0
votes
2
replies
1.0k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.2 years ago Gaia • 0
3
votes
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
3.2 years ago n.tear ▴ 20
1
vote
1
reply
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
6
votes
7
replies
1.7k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 3.4 years ago by 42k • written 3.5 years ago by ▴ 20
0
votes
4
replies
1.6k
views
Calculating per-exon PSI from DEXSeq
DEXSeq
3.8 years ago Angel Liang • 0
1
vote
2
replies
1.2k
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 3.8 years ago by ★ 1.9k • written 3.8 years ago by • 0
0
votes
2
replies
896
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 3.8 years ago by ★ 3.7k • written 3.8 years ago by • 0
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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