Showing : DEXSeq • reset
0
votes
0
replies
87
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
4 weeks ago cftattersfield • 0
0
votes
1
reply
381
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 7 months ago by ★ 4.7k • written 7 months ago by • 0
2
votes
1
reply
524
views
How to design DEXSeq formula for multiple variables
DEXSeq
9 months ago • updated 8 months ago Sara • 0
3
votes
1
reply
612
views
How to save the DEXSeq results
DEXSeq
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
0
replies
331
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
10 months ago Sara • 0
0
votes
3
replies
579
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
0
votes
1
reply
447
views
Adding columns to DEXSeqResults object
DEXSeq
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
0
votes
1
reply
799
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
0
replies
376
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
11 months ago jean-christophe.helbling • 0
2
votes
4
replies
843
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
13 months ago • updated 12 months ago thomas.heigl.ibk • 0
0
votes
2
replies
665
views
Swimming downstream: transcript fold changes
DEXSeq stageR
16 months ago jbono ▴ 10
1
vote
1
reply
710
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
16 months ago NiKo ▴ 10
0
votes
3
replies
1.1k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 18 months ago by ★ 1.9k • written 18 months ago by • 0
0
votes
3
replies
1.3k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 18 months ago by 16k • written 19 months ago by • 0
0
votes
2
replies
962
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
19 months ago • updated 18 months ago yr542 • 0
8
votes
7
replies
2.5k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 20 months ago by ▴ 20 • written 2.4 years ago by ▴ 20
1
vote
5
replies
1.3k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 20 months ago by ★ 1.9k • written 20 months ago by • 0
0
votes
0
replies
660
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
21 months ago nick_brittain55 • 0
0
votes
0
replies
591
views
Error while performing DEXseq
DEXSeq
21 months ago vipul14 • 0
0
votes
0
replies
599
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
24 months ago Ben J ▴ 20
2
votes
2
replies
1.5k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.1 years ago Ben J ▴ 20
0
votes
0
replies
828
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
1
reply
1.0k
views
plotDEXSeq error?
DEXSeq dex
2.3 years ago barrypraveen • 0
1
vote
4
replies
1.3k
views
DEXseq batch removal
DEXSeq
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by ▴ 10
0
votes
0
replies
577
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.5 years ago Matthias Munz ▴ 20
0
votes
0
replies
689
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.6 years ago osieman52 • 0
1
vote
2
replies
1.1k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
2.6 years ago Delta._.43 ▴ 20
0
votes
1
reply
1.2k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.8 years ago NIK • 0
0
votes
4
replies
2.1k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.8 years ago by ▴ 90 • written 2.8 years ago by • 0
0
votes
5
replies
2.3k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.9 years ago by • 0
8
votes
12
replies
4.2k
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 9 months ago by ▴ 30 • written 2.9 years ago by ▴ 380
3
votes
2
replies
1.4k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.9 years ago • updated 2.8 years ago Dakarai ▴ 10
1
vote
1
reply
899
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.9 years ago by ★ 1.9k • written 3.0 years ago by • 0
1
vote
2
replies
1.2k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.3 years ago • updated 3.1 years ago A ▴ 40
3
votes
3
replies
1.4k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 120
0
votes
1
reply
1.1k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 3.1 years ago by ★ 1.9k • written 3.4 years ago by • 0
1
vote
1
reply
1.4k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3.1 years ago by ★ 1.9k • written 3.5 years ago by ▴ 10
2
votes
7
replies
1.7k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.5 years ago rbenel ▴ 40
0
votes
5
replies
1.6k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.6 years ago bioinformatic_trainee ▴ 10
1
vote
0
replies
1.4k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.6 years ago Matthias Munz ▴ 20
0
votes
0
replies
853
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.6 years ago n.tear ▴ 20
0
votes
0
replies
833
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.7 years ago Matthias Munz ▴ 20
1
vote
6
replies
2.0k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.7 years ago by ▴ 120 • written 3.9 years ago by ▴ 10
4
votes
5
replies
2.5k
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
3.8 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.1k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.9 years ago jbono ▴ 10
0
votes
2
replies
1.3k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
4.0 years ago • updated 3.9 years ago Gaia • 0
3
votes
2
replies
1.4k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
4.0 years ago Angel ▴ 10
2
votes
2
replies
1.5k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.0 years ago n.tear ▴ 20
1
vote
1
reply
1.3k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 4.2 years ago by ★ 1.9k • written 4.2 years ago by • 0
0
votes
2
replies
1.6k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
4.7 years ago • updated 4.3 years ago aleksandar.baburski.g • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
Awards • All
Popular Question to svlachavas ▴ 840
Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.1k
Popular Question to Marco • 0
Locations • All
USA, 13 minutes ago
Pittsburgh, United States, 34 minutes ago
United States, 1 hour ago
Seattle, WA, United States, 1 hour ago
UPF, Barcelona, Spain, 1 hour ago
Traffic: 1383 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6