Showing : DEXSEq • reset
2
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227
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How to design DEXSeq formula for multiple variables
DEXSeq
7 weeks ago • updated 23 days ago Sara • 0
3
votes
1
reply
233
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How to save the DEXSeq results
DEXSeq
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
0
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0
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143
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
10 weeks ago • updated 9 weeks ago Sara • 0
0
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3
replies
253
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 weeks ago by ★ 1.9k • written 11 weeks ago by • 0
0
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1
reply
216
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Adding columns to DEXSeqResults object
DEXSeq
updated 11 weeks ago by ★ 1.9k • written 11 weeks ago by • 0
0
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1
reply
214
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by • 0
0
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0
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194
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
3 months ago jean-christophe.helbling • 0
2
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4
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525
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
5 months ago • updated 4 months ago thomas.heigl.ibk • 0
0
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2
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440
views
Swimming downstream: transcript fold changes
DEXSeq stageR
8 months ago jbono ▴ 10
1
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1
reply
480
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
8 months ago NiKo ▴ 10
0
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3
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769
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
0
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3
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917
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 10 months ago by 16k • written 11 months ago by • 0
0
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2
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637
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
11 months ago • updated 10 months ago yr542 • 0
8
votes
7
replies
2.0k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 12 months ago by ▴ 20 • written 20 months ago by ▴ 20
1
vote
5
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952
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 12 months ago by ★ 1.9k • written 12 months ago by • 0
0
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0
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449
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
13 months ago nick_brittain55 • 0
0
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0
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452
views
Error while performing DEXseq
DEXSeq
13 months ago vipul14 • 0
0
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0
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459
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
16 months ago Ben J ▴ 20
2
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2
replies
1.1k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
17 months ago Ben J ▴ 20
0
votes
0
replies
636
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 19 months ago by 42k • written 19 months ago by • 0
0
votes
1
reply
856
views
plotDEXSeq error?
DEXSeq dex
19 months ago barrypraveen • 0
1
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4
replies
1.0k
views
DEXseq batch removal
DEXSeq
updated 21 months ago by ★ 1.9k • written 21 months ago by ▴ 10
0
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0
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454
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
22 months ago Matthias Munz ▴ 10
0
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0
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543
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
23 months ago osieman52 • 0
1
vote
2
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890
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
23 months ago Delta._.43 ▴ 20
0
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1
reply
934
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.1 years ago NIK • 0
0
votes
4
replies
1.6k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.1 years ago by ▴ 90 • written 2.2 years ago by • 0
0
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5
replies
2.0k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.2 years ago by • 0
7
votes
12
replies
3.4k
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 5 weeks ago by ▴ 30 • written 2.2 years ago by ▴ 370
3
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2
replies
1.0k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.3 years ago • updated 2.2 years ago Dakarai ▴ 10
1
vote
1
reply
709
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by • 0
1
vote
2
replies
928
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.6 years ago • updated 2.4 years ago A ▴ 40
3
votes
3
replies
1.2k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.5 years ago by 42k • written 2.5 years ago by ▴ 120
0
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1
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902
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.4 years ago by ★ 1.9k • written 2.7 years ago by • 0
1
vote
1
reply
1.2k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.4 years ago by ★ 1.9k • written 2.9 years ago by ▴ 10
2
votes
7
replies
1.4k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
2.9 years ago • updated 2.8 years ago rbenel ▴ 40
0
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5
replies
1.3k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.9 years ago bioinformatic_trainee ▴ 10
0
votes
0
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921
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.9 years ago Matthias Munz ▴ 10
0
votes
0
replies
681
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.0 years ago n.tear ▴ 20
0
votes
0
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681
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.0 years ago Matthias Munz ▴ 10
1
vote
6
replies
1.6k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.1 years ago by ▴ 120 • written 3.2 years ago by ▴ 10
4
votes
5
replies
2.1k
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
3.2 years ago Matthias Munz ▴ 10
0
votes
0
replies
915
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.3 years ago jbono ▴ 10
0
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2
replies
1.1k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.3 years ago Gaia • 0
3
votes
2
replies
1.1k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.3 years ago Angel ▴ 10
2
votes
2
replies
1.2k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.4 years ago • updated 3.3 years ago n.tear ▴ 20
1
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1
reply
1.1k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3.5 years ago by ★ 1.9k • written 3.5 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
4.0 years ago • updated 3.6 years ago aleksandar.baburski.g • 0
1
vote
6
replies
4.1k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.6 years ago by ▴ 20 • written 9.3 years ago by • 0
0
votes
2
replies
1.5k
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 3.6 years ago by ▴ 20 • written 6.5 years ago by • 0
50 results • Page 1 of 1
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Comment: limma comparison for small sample size and how to get covariance matrix by Gordon Smyth 51k
Your MDS plot is better than before, but you are still not following the recommendation for making for making such plots given in the limma…
Comment: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
Also, ``` > result <- mapUniProt( from = "EMBL-GenBank-DDBJ_CDS", to = "UniProtKB", query = c("ACF95883.1") ) > result From…
Comment: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
Ugh, here's the link https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Cre…
Answer: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.
Answer: XCMS2 of orbitrap data by Elodie • 0
Hi, I have the same question, I have acquired MS2 data with PRM analysis and inclusion lists of several ions. I have a list of product ion…
Votes
Answer: EPIC array hg38 annotation?
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
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