Showing : DEXseq • reset
0
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279
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 3 months ago by ★ 4.5k • written 3 months ago by • 0
2
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1
reply
390
views
How to design DEXSeq formula for multiple variables
DEXSeq
5 months ago • updated 4 months ago Sara • 0
3
votes
1
reply
438
views
How to save the DEXSeq results
DEXSeq
updated 6 months ago by 42k • written 6 months ago by • 0
0
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0
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270
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
6 months ago Sara • 0
0
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3
replies
437
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 months ago by ★ 1.9k • written 6 months ago by • 0
0
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1
reply
357
views
Adding columns to DEXSeqResults object
DEXSeq
updated 6 months ago by ★ 1.9k • written 6 months ago by • 0
0
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1
reply
522
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 6 months ago by 42k • written 6 months ago by • 0
0
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0
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310
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
8 months ago jean-christophe.helbling • 0
2
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4
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710
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
9 months ago • updated 8 months ago thomas.heigl.ibk • 0
0
votes
2
replies
576
views
Swimming downstream: transcript fold changes
DEXSeq stageR
12 months ago jbono ▴ 10
1
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1
reply
615
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
12 months ago NiKo ▴ 10
0
votes
3
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949
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 14 months ago by ★ 1.9k • written 14 months ago by • 0
0
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3
replies
1.1k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 15 months ago by 16k • written 15 months ago by • 0
0
votes
2
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822
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
15 months ago • updated 14 months ago yr542 • 0
8
votes
7
replies
2.3k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 16 months ago by ▴ 20 • written 2.0 years ago by ▴ 20
1
vote
5
replies
1.1k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 16 months ago by ★ 1.9k • written 16 months ago by • 0
0
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0
replies
591
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
17 months ago nick_brittain55 • 0
0
votes
0
replies
540
views
Error while performing DEXseq
DEXSeq
17 months ago vipul14 • 0
0
votes
0
replies
549
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
20 months ago Ben J ▴ 20
2
votes
2
replies
1.3k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
21 months ago Ben J ▴ 20
0
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0
replies
752
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 23 months ago by 42k • written 23 months ago by • 0
0
votes
1
reply
963
views
plotDEXSeq error?
DEXSeq dex
23 months ago barrypraveen • 0
1
vote
4
replies
1.1k
views
DEXseq batch removal
DEXSeq
updated 2.1 years ago by ★ 1.9k • written 2.1 years ago by ▴ 10
0
votes
0
replies
515
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.2 years ago Matthias Munz ▴ 20
0
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0
replies
635
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.2 years ago osieman52 • 0
1
vote
2
replies
1.0k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
2.2 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
2.5 years ago • updated 2.4 years ago NIK • 0
0
votes
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 2.5 years ago by • 0
0
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5
replies
2.2k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.6 years ago by • 0
7
votes
12
replies
3.8k
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 months ago by ▴ 30 • written 2.6 years ago by ▴ 380
3
votes
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
2.6 years ago • updated 2.5 years ago Dakarai ▴ 10
1
vote
1
reply
824
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.6 years ago by ★ 1.9k • written 2.6 years ago by • 0
1
vote
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
votes
3
replies
1.3k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.8 years ago by 42k • written 2.8 years ago by ▴ 120
0
votes
1
reply
1.0k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.8 years ago by ★ 1.9k • written 3.1 years ago by • 0
1
vote
1
reply
1.3k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.8 years ago by ★ 1.9k • written 3.2 years ago by ▴ 10
2
votes
7
replies
1.6k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.2 years ago rbenel ▴ 40
0
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5
replies
1.5k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.2 years ago bioinformatic_trainee ▴ 10
1
vote
0
replies
1.2k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.3 years ago Matthias Munz ▴ 20
0
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0
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787
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.3 years ago n.tear ▴ 20
0
votes
0
replies
764
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.4 years ago Matthias Munz ▴ 20
1
vote
6
replies
1.8k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.4 years ago by ▴ 120 • written 3.6 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
3.5 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.0k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.6 years ago jbono ▴ 10
0
votes
2
replies
1.2k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.6 years ago Gaia • 0
3
votes
2
replies
1.2k
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
3.7 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 3.9 years ago by ★ 1.9k • written 3.9 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
4.4 years ago • updated 4.0 years ago aleksandar.baburski.g • 0
1
vote
6
replies
4.3k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 4.0 years ago by ▴ 20 • written 9.6 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Answer: Differential Expression Analysis with unbalanced batches without replication bet by Gordon Smyth 51k
> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected. by Adam • 0
I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…
Comment: Problem at champ.load by icecreamlover • 0
Hello! Were you able to figure this out? I am running into the same error!
Comment: ChAMP - obtaining beta values using EPICv2 annotation by icecreamlover • 0
Hello, Were you able to fix the error? I used the same document and I am running into the same error. I am curious if you have any feedba…
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