Showing : dexseq • reset
2
votes
1
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57
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How to design DEXSeq formula for multiple variables
DEXSeq
updated 2 days ago by ★ 1.9k • written 4 days ago by • 0
3
votes
1
reply
145
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How to save the DEXSeq results
DEXSeq
updated 11 days ago by 42k • written 11 days ago by • 0
0
votes
0
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99
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
23 days ago • updated 18 days ago Sara • 0
0
votes
3
replies
185
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 16 days ago by ★ 1.9k • written 29 days ago by • 0
0
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1
reply
165
views
Adding columns to DEXSeqResults object
DEXSeq
updated 28 days ago by ★ 1.9k • written 4 weeks ago by • 0
0
votes
1
reply
124
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 28 days ago by 42k • written 29 days 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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442
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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
replies
392
views
Swimming downstream: transcript fold changes
DEXSeq stageR
6 months ago jbono ▴ 10
1
vote
1
reply
412
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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688
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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
3
replies
806
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 9 months ago by 16k • written 9 months ago by • 0
0
votes
2
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582
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
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
5
replies
881
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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397
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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
replies
408
views
Error while performing DEXseq
DEXSeq
11 months ago vipul14 • 0
0
votes
0
replies
432
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
14 months ago Ben J • 0
0
votes
2
replies
919
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
15 months ago Ben J • 0
0
votes
0
replies
588
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 17 months ago by 42k • written 17 months ago by • 0
0
votes
1
reply
814
views
plotDEXSeq error?
DEXSeq dex
18 months ago • updated 17 months ago barrypraveen • 0
1
vote
4
replies
956
views
DEXseq batch removal
DEXSeq
updated 19 months ago by ★ 1.9k • written 19 months ago by ▴ 10
0
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0
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430
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
20 months ago Matthias Munz ▴ 10
0
votes
0
replies
514
views
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
863
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
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
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
663
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
883
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.5 years ago • updated 2.3 years ago A ▴ 40
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
0
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1
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858
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
votes
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
replies
648
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.9 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
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
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
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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
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
replies
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
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Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
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Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
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Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
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@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
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Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
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
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