Showing : DEXseq • reset
2
votes
1
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222
views
How to design DEXSeq formula for multiple variables
DEXSeq
7 weeks ago • updated 20 days ago Sara • 0
3
votes
1
reply
230
views
How to save the DEXSeq results
DEXSeq
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
0
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0
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140
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
10 weeks ago • updated 9 weeks ago Sara • 0
0
votes
3
replies
250
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 weeks ago by ★ 1.9k • written 10 weeks ago by • 0
0
votes
1
reply
214
views
Adding columns to DEXSeqResults object
DEXSeq
updated 10 weeks ago by ★ 1.9k • written 11 weeks ago by • 0
0
votes
1
reply
207
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 10 weeks ago by 42k • written 10 weeks ago by • 0
0
votes
0
replies
191
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
3 months ago jean-christophe.helbling • 0
2
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4
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518
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
5 months ago • updated 4 months ago thomas.heigl.ibk • 0
0
votes
2
replies
437
views
Swimming downstream: transcript fold changes
DEXSeq stageR
7 months ago jbono ▴ 10
1
vote
1
reply
478
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
8 months ago NiKo ▴ 10
0
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3
replies
762
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
0
votes
3
replies
914
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 10 months ago by 16k • written 11 months ago by • 0
0
votes
2
replies
637
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
10 months ago • updated 9 months ago yr542 • 0
8
votes
7
replies
1.9k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 12 months ago by ▴ 20 • written 20 months ago by ▴ 20
1
vote
5
replies
942
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 12 months ago by ★ 1.9k • written 12 months ago by • 0
0
votes
0
replies
447
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
13 months ago nick_brittain55 • 0
0
votes
0
replies
447
views
Error while performing DEXseq
DEXSeq
13 months ago vipul14 • 0
0
votes
0
replies
455
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
15 months ago Ben J ▴ 20
2
votes
2
replies
1.0k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
17 months ago Ben J ▴ 20
0
votes
0
replies
632
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 19 months ago by 42k • written 19 months ago by • 0
0
votes
1
reply
854
views
plotDEXSeq error?
DEXSeq dex
19 months ago barrypraveen • 0
1
vote
4
replies
1.0k
views
DEXseq batch removal
DEXSeq
updated 20 months ago by ★ 1.9k • written 21 months ago by ▴ 10
0
votes
0
replies
454
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
22 months ago Matthias Munz ▴ 10
0
votes
0
replies
541
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
23 months ago osieman52 • 0
1
vote
2
replies
889
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
23 months ago Delta._.43 ▴ 20
0
votes
1
reply
932
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.1 years ago NIK • 0
0
votes
4
replies
1.6k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.1 years ago by ▴ 90 • written 2.2 years ago by • 0
0
votes
5
replies
2.0k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.2 years ago by • 0
7
votes
12
replies
3.3k
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 5 weeks ago by ▴ 30 • written 2.2 years ago by ▴ 370
3
votes
2
replies
1.0k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.2 years ago Dakarai ▴ 10
1
vote
1
reply
705
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by • 0
1
vote
2
replies
924
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.6 years ago • updated 2.4 years ago A ▴ 40
3
votes
3
replies
1.2k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.5 years ago by 42k • written 2.5 years ago by ▴ 120
0
votes
1
reply
900
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.4 years ago by ★ 1.9k • written 2.7 years ago by • 0
1
vote
1
reply
1.2k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.4 years ago by ★ 1.9k • written 2.9 years ago by ▴ 10
2
votes
7
replies
1.4k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
2.9 years ago • updated 2.8 years ago rbenel ▴ 40
0
votes
5
replies
1.3k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.9 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
917
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.9 years ago Matthias Munz ▴ 10
0
votes
0
replies
679
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.0 years ago n.tear ▴ 20
0
votes
0
replies
676
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.0 years ago Matthias Munz ▴ 10
1
vote
6
replies
1.6k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.1 years ago by ▴ 120 • written 3.2 years ago by ▴ 10
4
votes
5
replies
2.0k
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
3.2 years ago Matthias Munz ▴ 10
0
votes
0
replies
912
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.2 years ago jbono ▴ 10
0
votes
2
replies
1.1k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.3 years ago Gaia • 0
3
votes
2
replies
1.1k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.3 years ago Angel ▴ 10
2
votes
2
replies
1.2k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.4 years ago • updated 3.3 years ago n.tear ▴ 20
1
vote
1
reply
1.1k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3.5 years ago by ★ 1.9k • written 3.5 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
4.0 years ago • updated 3.6 years ago aleksandar.baburski.g • 0
1
vote
6
replies
4.1k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.6 years ago by ▴ 20 • written 9.3 years ago by • 0
0
votes
2
replies
1.5k
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 3.6 years ago by ▴ 20 • written 6.5 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ranking the GSEA Results by Lluís Revilla Sancho ▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction by Antonio • 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results by alserg ▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results by alserg ▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Votes
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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