Showing : DEXSEq • reset
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300
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 4 months ago by ★ 4.6k • written 4 months ago by • 0
2
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1
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413
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How to design DEXSeq formula for multiple variables
DEXSeq
6 months ago • updated 5 months ago Sara • 0
3
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1
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466
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How to save the DEXSeq results
DEXSeq
updated 7 months ago by 43k • written 7 months ago by • 0
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0
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286
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
7 months ago Sara • 0
0
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3
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470
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 7 months ago by ★ 1.9k • written 7 months ago by • 0
0
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1
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372
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Adding columns to DEXSeqResults object
DEXSeq
updated 7 months ago by ★ 1.9k • written 7 months ago by • 0
0
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1
reply
567
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 7 months ago by 43k • written 7 months ago by • 0
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0
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327
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DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
8 months ago jean-christophe.helbling • 0
2
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4
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730
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
10 months ago • updated 9 months ago thomas.heigl.ibk • 0
0
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2
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598
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Swimming downstream: transcript fold changes
DEXSeq stageR
13 months ago jbono ▴ 10
1
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1
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635
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
13 months ago NiKo ▴ 10
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3
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964
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 15 months ago by ★ 1.9k • written 15 months ago by • 0
0
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3
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1.2k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 15 months ago by 16k • written 16 months ago by • 0
0
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2
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851
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DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
16 months ago • updated 15 months ago yr542 • 0
8
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7
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2.3k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 17 months ago by ▴ 20 • written 2.1 years ago by ▴ 20
1
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5
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1.2k
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DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 17 months ago by ★ 1.9k • written 17 months ago by • 0
0
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0
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604
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
18 months ago nick_brittain55 • 0
0
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0
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552
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Error while performing DEXseq
DEXSeq
18 months ago vipul14 • 0
0
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0
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557
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
21 months ago Ben J ▴ 20
2
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2
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1.3k
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
22 months ago Ben J ▴ 20
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0
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768
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DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
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1
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981
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plotDEXSeq error?
DEXSeq dex
2.0 years ago barrypraveen • 0
1
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4
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1.2k
views
DEXseq batch removal
DEXSeq
updated 2.1 years ago by ★ 1.9k • written 2.1 years ago by ▴ 10
0
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0
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532
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.2 years ago Matthias Munz ▴ 20
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0
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648
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.3 years ago osieman52 • 0
1
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2
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1.0k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
2.3 years ago Delta._.43 ▴ 20
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1
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1.1k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.5 years ago NIK • 0
0
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4
replies
1.9k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.5 years ago by ▴ 90 • written 2.6 years ago by • 0
0
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5
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2.2k
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DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.7 years ago by • 0
8
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12
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3.9k
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 6 months ago by ▴ 30 • written 2.6 years ago by ▴ 380
3
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2
replies
1.2k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.7 years ago • updated 2.6 years ago Dakarai ▴ 10
1
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1
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842
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Increased number of exons in DEXSeq
DEXSeq exon
updated 2.7 years ago by ★ 1.9k • written 2.7 years ago by • 0
1
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2
replies
1.1k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.0 years ago • updated 2.8 years ago A ▴ 40
3
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3
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1.3k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 120
0
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1
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1.0k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.9 years ago by ★ 1.9k • written 3.1 years ago by • 0
1
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1
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1.4k
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DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.9 years ago by ★ 1.9k • written 3.3 years ago by ▴ 10
2
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7
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1.6k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.3 years ago • updated 3.2 years ago rbenel ▴ 40
0
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5
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1.5k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.3 years ago bioinformatic_trainee ▴ 10
1
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0
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1.3k
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.4 years ago Matthias Munz ▴ 20
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0
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797
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.4 years ago n.tear ▴ 20
0
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0
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775
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DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.4 years ago Matthias Munz ▴ 20
1
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6
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1.8k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.5 years ago by ▴ 120 • written 3.7 years ago by ▴ 10
4
votes
5
replies
2.3k
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
3.6 years ago Matthias Munz ▴ 20
0
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0
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1.1k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.7 years ago jbono ▴ 10
0
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2
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1.2k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.7 years ago Gaia • 0
3
votes
2
replies
1.3k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.7 years ago Angel ▴ 10
2
votes
2
replies
1.4k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.8 years ago • updated 3.7 years ago n.tear ▴ 20
1
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1
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1.2k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3.9 years ago by ★ 1.9k • written 3.9 years ago by • 0
0
votes
2
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1.5k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
4.4 years ago • updated 4.0 years ago aleksandar.baburski.g • 0
1
vote
6
replies
4.4k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 4.1 years ago by ▴ 20 • written 9.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd by liu.n • 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
> dim(spe) [1] 19962 425
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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