Showing : dexseq • reset
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319
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 5 months ago by ★ 4.6k • written 5 months ago by • 0
2
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1
reply
433
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How to design DEXSeq formula for multiple variables
DEXSeq
7 months ago • updated 6 months ago Sara • 0
3
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1
reply
502
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How to save the DEXSeq results
DEXSeq
updated 7 months ago by 43k • written 7 months ago by • 0
0
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0
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297
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
8 months ago Sara • 0
0
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3
replies
503
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 8 months ago by ★ 1.9k • written 8 months ago by • 0
0
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1
reply
397
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Adding columns to DEXSeqResults object
DEXSeq
updated 8 months ago by ★ 1.9k • written 8 months ago by • 0
0
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1
reply
626
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 8 months ago by 43k • written 8 months ago by • 0
0
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0
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340
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
9 months ago jean-christophe.helbling • 0
2
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4
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765
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
11 months ago • updated 10 months ago thomas.heigl.ibk • 0
0
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2
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614
views
Swimming downstream: transcript fold changes
DEXSeq stageR
13 months ago jbono ▴ 10
1
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1
reply
660
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
14 months ago NiKo ▴ 10
0
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3
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992
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 16 months ago by ★ 1.9k • written 16 months ago by • 0
0
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3
replies
1.2k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 16 months ago by 16k • written 17 months ago by • 0
0
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2
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872
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DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
16 months ago yr542 • 0
8
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7
replies
2.4k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 18 months ago by ▴ 20 • written 2.2 years ago by ▴ 20
1
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5
replies
1.2k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 18 months ago by ★ 1.9k • written 18 months ago by • 0
0
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0
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621
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
19 months ago nick_brittain55 • 0
0
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0
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562
views
Error while performing DEXseq
DEXSeq
19 months ago vipul14 • 0
0
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0
replies
564
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
21 months ago Ben J ▴ 20
2
votes
2
replies
1.4k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
23 months ago Ben J ▴ 20
0
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0
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785
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
votes
1
reply
1.0k
views
plotDEXSeq error?
DEXSeq dex
2.1 years ago barrypraveen • 0
1
vote
4
replies
1.2k
views
DEXseq batch removal
DEXSeq
updated 2.2 years ago by ★ 1.9k • written 2.2 years ago by ▴ 10
0
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0
replies
539
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.3 years ago Matthias Munz ▴ 20
0
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0
replies
661
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.4 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
2.4 years ago Delta._.43 ▴ 20
0
votes
1
reply
1.1k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.6 years ago NIK • 0
0
votes
4
replies
2.0k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.6 years ago by ▴ 90 • written 2.7 years ago by • 0
0
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5
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2.3k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.7 years ago by • 0
8
votes
12
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4.0k
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 7 months ago by ▴ 30 • written 2.7 years ago by ▴ 380
3
votes
2
replies
1.3k
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 Dakarai ▴ 10
1
vote
1
reply
861
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.8 years ago by ★ 1.9k • written 2.8 years ago by • 0
1
vote
2
replies
1.2k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.1 years ago • updated 2.9 years ago A ▴ 40
3
votes
3
replies
1.4k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 120
0
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1
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1.1k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.9 years ago by ★ 1.9k • written 3.2 years ago by • 0
1
vote
1
reply
1.4k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.9 years ago by ★ 1.9k • written 3.4 years ago by ▴ 10
2
votes
7
replies
1.6k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.4 years ago • updated 3.3 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
3.4 years ago bioinformatic_trainee ▴ 10
1
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0
replies
1.3k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.4 years ago Matthias Munz ▴ 20
0
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0
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811
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.5 years ago n.tear ▴ 20
0
votes
0
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787
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.5 years ago Matthias Munz ▴ 20
1
vote
6
replies
1.9k
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
2.4k
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
3.7 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.1k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.7 years ago jbono ▴ 10
0
votes
2
replies
1.3k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.8 years ago Gaia • 0
3
votes
2
replies
1.3k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.8 years ago Angel ▴ 10
2
votes
2
replies
1.4k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.9 years ago • updated 3.8 years ago n.tear ▴ 20
1
vote
1
reply
1.2k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 4.0 years ago by ★ 1.9k • written 4.0 years ago by • 0
0
votes
2
replies
1.5k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
4.5 years ago • updated 4.1 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 9.8 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k
Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0
But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…
Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0
After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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