Showing : DEXSEq • reset
0
votes
2
replies
160
views
Swimming downstream: transcript fold changes
DEXSeq stageR
4 weeks ago jbono ▴ 10
0
votes
1
reply
159
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
5 weeks ago NiKo • 0
0
votes
3
replies
421
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 3 months ago by ★ 1.9k • written 3 months ago by • 0
0
votes
3
replies
500
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 4 months ago by 16k • written 4 months ago by • 0
0
votes
2
replies
334
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
4 months ago • updated 3 months ago yr542 • 0
8
votes
7
replies
1.4k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 5 months ago by ▴ 20 • written 13 months ago by ▴ 20
1
vote
5
replies
592
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 5 months ago by ★ 1.9k • written 5 months ago by • 0
0
votes
0
replies
242
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
6 months ago nick_brittain55 • 0
0
votes
0
replies
254
views
Error while performing DEXseq
DEXSeq
6 months ago vipul14 • 0
0
votes
0
replies
290
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
9 months ago Ben J • 0
0
votes
2
replies
612
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
10 months ago Ben J • 0
0
votes
0
replies
409
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 12 months ago by 41k • written 12 months ago by • 0
0
votes
1
reply
614
views
plotDEXSeq error?
DEXSeq dex
12 months ago barrypraveen • 0
1
vote
4
replies
754
views
DEXseq batch removal
DEXSeq
updated 14 months ago by ★ 1.9k • written 14 months ago by ▴ 10
0
votes
0
replies
322
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
15 months ago Matthias Munz ▴ 10
0
votes
0
replies
379
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
16 months ago osieman52 • 0
1
vote
2
replies
650
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
16 months ago Delta._.43 ▴ 20
0
votes
1
reply
659
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
18 months ago NIK • 0
0
votes
4
replies
1.1k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 18 months ago by ▴ 90 • written 19 months ago by • 0
0
votes
5
replies
1.7k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 4.7 years ago by • 0
6
votes
11
replies
2.4k
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 8 months ago by • 0 • written 20 months ago by ▴ 350
3
votes
2
replies
752
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
20 months ago • updated 19 months ago Dakarai ▴ 10
1
vote
1
reply
527
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 20 months ago by ★ 1.9k • written 20 months ago by • 0
1
vote
2
replies
723
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.0 years ago • updated 22 months ago A ▴ 40
3
votes
3
replies
893
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 23 months ago by 41k • written 23 months ago by ▴ 120
0
votes
1
reply
711
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 22 months ago by ★ 1.9k • written 2.2 years ago by • 0
1
vote
1
reply
912
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 22 months ago by ★ 1.9k • written 2.3 years ago by ▴ 10
2
votes
7
replies
1.1k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
2.3 years ago rbenel ▴ 30
0
votes
5
replies
1.0k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.3 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
671
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.4 years ago Matthias Munz ▴ 10
0
votes
0
replies
522
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
2.4 years ago n.tear ▴ 20
0
votes
0
replies
532
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.5 years ago Matthias Munz ▴ 10
1
vote
6
replies
1.3k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 2.5 years ago by ▴ 120 • written 2.7 years ago by ▴ 10
4
votes
5
replies
1.6k
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
2.6 years ago Matthias Munz ▴ 10
0
votes
0
replies
712
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
2.7 years ago jbono ▴ 10
0
votes
2
replies
844
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
2.7 years ago Gaia • 0
3
votes
2
replies
863
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
2.8 years ago • updated 2.7 years ago Angel ▴ 10
2
votes
2
replies
1.0k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
2.8 years ago • updated 2.7 years ago n.tear ▴ 20
1
vote
1
reply
827
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 2.9 years ago by ★ 1.9k • written 2.9 years ago by • 0
0
votes
2
replies
1.0k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
3.5 years ago • updated 3.1 years ago aleksandar.baburski.g • 0
1
vote
6
replies
3.7k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.1 years ago by ▴ 20 • written 8.7 years ago by • 0
0
votes
2
replies
1.3k
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 3.1 years ago by ▴ 20 • written 5.9 years ago by • 0
6
votes
7
replies
1.5k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 3.0 years ago by 41k • written 3.1 years ago by ▴ 20
0
votes
2
replies
721
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 3.4 years ago by ★ 3.7k • written 3.4 years ago by • 0
0
votes
4
replies
1.3k
views
Calculating per-exon PSI from DEXSeq
DEXSeq
3.4 years ago Angel Liang • 0
1
vote
2
replies
989
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 3.4 years ago by ★ 1.9k • written 3.4 years ago by • 0
0
votes
1
reply
611
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 3.4 years ago by 41k • written 3.4 years ago by ▴ 10
1
vote
2
replies
976
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq estimateDispersions
3.5 years ago aleksandar.baburski.g • 0
0
votes
2
replies
751
views
DEXSeq HTML report Error
DEXSeq
updated 3.5 years ago by 3.9k • written 3.5 years ago by • 0
0
votes
0
replies
565
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
3.6 years ago alexis.weinreb • 0
50 results • Page 1 of 1
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Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0
Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…
Answer: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k
You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model. …
Answer: Agilent Microarray Gene Oncology analysis gone wrong by Gordon Smyth 49k
Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…
Comment: Normalised counts from RUVg in RUVSeq by Shaimaa Gamal • 0
Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
Comment: enrichGOgradient color change by James W. MacDonald 64k
You could look at my answer and extrapolate from there.
Votes
Answer: Correct the batch effect in methylation analysis in R
Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
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