Showing : DEXSEq • reset
3
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1
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100
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How to save the DEXSeq results
DEXSeq
updated 3 days ago by 42k • written 3 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
15 days ago • updated 10 days ago Sara • 0
0
votes
3
replies
176
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 days ago by ★ 1.9k • written 21 days ago by • 0
0
votes
1
reply
161
views
Adding columns to DEXSeqResults object
DEXSeq
updated 21 days ago by ★ 1.9k • written 22 days ago by • 0
0
votes
1
reply
114
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 21 days ago by 42k • written 21 days ago by • 0
0
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0
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136
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
8 weeks ago jean-christophe.helbling • 0
2
votes
4
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421
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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
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Swimming downstream: transcript fold changes
DEXSeq stageR
6 months ago jbono ▴ 10
1
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1
reply
393
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
6 months ago NiKo ▴ 10
0
votes
3
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663
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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
788
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 9 months ago by 16k • written 9 months ago by • 0
0
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2
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566
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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 18 months ago by ▴ 20
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
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0
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387
views
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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401
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Error while performing DEXseq
DEXSeq
11 months ago vipul14 • 0
0
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0
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427
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
14 months ago Ben J • 0
0
votes
2
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905
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
15 months ago Ben J • 0
0
votes
0
replies
580
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 17 months ago by 42k • written 17 months ago by • 0
0
votes
1
reply
806
views
plotDEXSeq error?
DEXSeq dex
17 months ago barrypraveen • 0
1
vote
4
replies
939
views
DEXseq batch removal
DEXSeq
updated 19 months ago by ★ 1.9k • written 19 months ago by ▴ 10
0
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0
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422
views
DEXSeq: mcols(dxd)$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
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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
0
votes
5
replies
1.9k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.1 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
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
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
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
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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
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
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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
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
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
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 9.1 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 6.3 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
50 results • Page 1 of 1
Recent ...
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma by Shaimaa Gamal • 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Comment: DSS CpG coverage threshold by j.gilbert • 0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
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