Showing : Dexseq • reset
0
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240
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 11 weeks ago by ★ 4.5k • written 11 weeks ago by • 0
2
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1
reply
353
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How to design DEXSeq formula for multiple variables
DEXSeq
4 months ago • updated 3 months ago Sara • 0
3
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1
reply
397
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How to save the DEXSeq results
DEXSeq
updated 5 months ago by 42k • written 5 months ago by • 0
0
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0
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245
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
5 months ago Sara • 0
0
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3
replies
402
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 5 months ago by ★ 1.9k • written 5 months ago by • 0
0
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1
reply
319
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Adding columns to DEXSeqResults object
DEXSeq
updated 5 months ago by ★ 1.9k • written 5 months ago by • 0
0
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1
reply
446
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 months ago by 42k • written 5 months ago by • 0
0
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0
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272
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
6 months ago jean-christophe.helbling • 0
2
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4
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672
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
8 months ago • updated 7 months ago thomas.heigl.ibk • 0
0
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2
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542
views
Swimming downstream: transcript fold changes
DEXSeq stageR
11 months ago jbono ▴ 10
1
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1
reply
599
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
11 months ago NiKo ▴ 10
0
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3
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919
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 13 months ago by ★ 1.9k • written 13 months ago by • 0
0
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3
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1.1k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 14 months ago by 16k • written 14 months ago by • 0
0
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2
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780
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
14 months ago • updated 13 months ago yr542 • 0
8
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7
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2.2k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 15 months ago by ▴ 20 • written 23 months ago by ▴ 20
1
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5
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1.1k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 15 months ago by ★ 1.9k • written 15 months ago by • 0
0
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0
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561
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
16 months ago nick_brittain55 • 0
0
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0
replies
516
views
Error while performing DEXseq
DEXSeq
16 months ago vipul14 • 0
0
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0
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528
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
19 months ago Ben J ▴ 20
2
votes
2
replies
1.2k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
20 months ago Ben J ▴ 20
0
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0
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725
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 22 months ago by 42k • written 22 months ago by • 0
0
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1
reply
936
views
plotDEXSeq error?
DEXSeq dex
22 months ago barrypraveen • 0
1
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4
replies
1.1k
views
DEXseq batch removal
DEXSeq
updated 24 months ago by ★ 1.9k • written 24 months ago by ▴ 10
0
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0
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501
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.1 years ago Matthias Munz ▴ 20
0
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0
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614
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.2 years ago osieman52 • 0
1
vote
2
replies
982
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
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1
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1.0k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.4 years ago NIK • 0
0
votes
4
replies
1.8k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.4 years ago by ▴ 90 • written 2.4 years ago by • 0
0
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5
replies
2.2k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.5 years ago by • 0
7
votes
12
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3.7k
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 4 months ago by ▴ 30 • written 2.5 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
2.5 years ago • updated 2.4 years ago Dakarai ▴ 10
1
vote
1
reply
795
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.5 years ago by ★ 1.9k • written 2.5 years ago by • 0
1
vote
2
replies
1.0k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.9 years ago • updated 2.7 years ago A ▴ 40
3
votes
3
replies
1.3k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.7 years ago by 42k • written 2.7 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 2.7 years ago by ★ 1.9k • written 3.0 years ago by • 0
1
vote
1
reply
1.3k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.7 years ago by ★ 1.9k • written 3.1 years ago by ▴ 10
2
votes
7
replies
1.5k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.1 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
3.2 years ago • updated 3.1 years ago bioinformatic_trainee ▴ 10
1
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0
replies
1.1k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.2 years ago Matthias Munz ▴ 20
0
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0
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762
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.2 years ago n.tear ▴ 20
0
votes
0
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749
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.3 years ago Matthias Munz ▴ 20
1
vote
6
replies
1.8k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.3 years ago by ▴ 120 • written 3.5 years ago by ▴ 10
4
votes
5
replies
2.2k
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
3.4 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.0k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.5 years ago jbono ▴ 10
0
votes
2
replies
1.2k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.6 years ago • updated 3.5 years ago Gaia • 0
3
votes
2
replies
1.2k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.6 years ago Angel ▴ 10
2
votes
2
replies
1.3k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.6 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 3.8 years ago by ★ 1.9k • written 3.8 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
4.3 years ago • updated 3.9 years ago aleksandar.baburski.g • 0
1
vote
6
replies
4.3k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.9 years ago by ▴ 20 • written 9.5 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library by mercedeh.movassagh ▴ 20
Hi Maria, so what is the code you are using? By the 3rd way to conduct the analysis do you mean looking at the interaction model from part …
Comment: miRTarRnaseq library by María Calvo • 0
Hello, in line with the previous questions, when the miRNA-mRNA interaction analysis is performed (3 rd way to conduct the analysis), I obt…
Answer: heatmap with batch effect by James W. MacDonald 67k
You have only one condition in the second batch, so it's not possible to remove the batch effect. You can probably adjust for it somewhat, …
Answer: how do I convert an Ilumn IDREF to a CPG loci by James W. MacDonald 67k
``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame with 865859 rows and 3 columns ch…
Answer: Which input data is acceptable for MAST? by Andrew_McDavid ▴ 270
Not too familiar with SCT v2. If it also has a point-mass at zero and the non-zero component is roughly-symmetric, then it might work ok w…
Votes
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Comment: Convert HGVS Representation back to Reference Genome Coordinates
Answer: How to control batch effect if Group and batch are same?
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