Showing : DEXSEq • reset
3
votes
1
reply
99
views
How to save the DEXSeq results
DEXSeq
updated 2 days ago by 42k • written 2 days ago by • 0
0
votes
0
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91
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
14 days ago • updated 10 days ago Sara • 0
0
votes
3
replies
174
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 8 days ago by ★ 1.9k • written 21 days ago by • 0
0
votes
1
reply
114
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 20 days ago by 42k • written 21 days ago by • 0
0
votes
1
reply
161
views
Adding columns to DEXSeqResults object
DEXSeq
updated 20 days ago by ★ 1.9k • written 22 days ago by • 0
0
votes
0
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136
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
8 weeks ago jean-christophe.helbling • 0
2
votes
4
replies
421
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
3 months ago • updated 10 weeks ago thomas.heigl.ibk • 0
0
votes
2
replies
379
views
Swimming downstream: transcript fold changes
DEXSeq stageR
6 months ago jbono ▴ 10
1
vote
1
reply
393
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
6 months ago NiKo ▴ 10
0
votes
3
replies
662
views
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
replies
565
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
replies
788
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 9 months ago by 16k • written 9 months ago by • 0
1
vote
5
replies
863
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
votes
0
replies
387
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
11 months ago nick_brittain55 • 0
0
votes
0
replies
400
views
Error while performing DEXseq
DEXSeq
11 months ago vipul14 • 0
0
votes
0
replies
427
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
14 months ago Ben J • 0
0
votes
2
replies
905
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
15 months ago Ben J • 0
0
votes
0
replies
580
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 17 months ago by 42k • written 17 months ago by • 0
0
votes
1
reply
805
views
plotDEXSeq error?
DEXSeq dex
17 months ago barrypraveen • 0
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 18 months ago by ▴ 20
1
vote
4
replies
939
views
DEXseq batch removal
DEXSeq
updated 19 months ago by ★ 1.9k • written 19 months ago by ▴ 10
0
votes
0
replies
422
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
20 months ago Matthias Munz ▴ 10
0
votes
0
replies
500
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
21 months ago osieman52 • 0
1
vote
2
replies
830
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
844
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
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 23 months ago by ▴ 90 • written 2.0 years ago by • 0
6
votes
11
replies
3.0k
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 13 months ago by • 0 • written 2.1 years ago by ▴ 350
3
votes
2
replies
951
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
654
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.1 years ago by ★ 1.9k • written 2.1 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
870
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.5 years ago • updated 2.3 years ago A ▴ 40
0
votes
1
reply
848
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
replies
1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.7 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
833
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.8 years ago Matthias Munz ▴ 10
0
votes
0
replies
638
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
638
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
879
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
3.1 years ago Gaia • 0
3
votes
2
replies
1.0k
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
993
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
892
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
0
votes
1
reply
712
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 3.9 years ago by 42k • written 3.9 years ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: deseq2 results by sajadahmad41454 • 0
could you please tell me if the results are fine or not? ![pca summary][1] ![pca plot][2] [1]: /media/images/ee7d8693-bcbe-4a7a-a566-d3…
Answer: normalization using Deseq2 by ATpoint ★ 4.1k
counts(dds, normalized=TRUE)
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I have tried what you suggested. I started with methylation loci. I created segment1 and segment2 but how to combine them bec…
Comment: EGSEA usage with microarray data (with vooma)? by Chris • 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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