Showing : dexseq • reset
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220
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Make DEXSeq plot normal scale
DEXSeq Dexseq
updated 4 months ago by 68k • written 4 months ago by • 0
4
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6
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1.5k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 5 months ago by ★ 4.9k • written 6 months ago by • 0
0
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0
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274
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My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
7 months ago cftattersfield • 0
0
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1
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514
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Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 14 months ago by ★ 4.9k • written 14 months ago by • 0
2
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1
reply
732
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How to design DEXSeq formula for multiple variables
DEXSeq
16 months ago • updated 15 months ago Sara • 0
3
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1
reply
821
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How to save the DEXSeq results
DEXSeq
updated 16 months ago by 43k • written 16 months ago by • 0
0
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0
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461
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
16 months ago Sara • 0
0
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3
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779
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 16 months ago by ★ 1.9k • written 17 months ago by • 0
0
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1
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582
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Adding columns to DEXSeqResults object
DEXSeq
updated 17 months ago by ★ 1.9k • written 17 months ago by • 0
0
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1
reply
1.2k
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 17 months ago by 43k • written 17 months ago by • 0
0
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0
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453
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
18 months ago jean-christophe.helbling • 0
2
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4
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1.0k
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
19 months ago • updated 18 months ago thomas.heigl.ibk • 0
0
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2
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794
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Swimming downstream: transcript fold changes
DEXSeq stageR
22 months ago jbono ▴ 10
1
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1
reply
882
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
22 months ago NiKo ▴ 10
0
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3
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1.2k
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 2.0 years ago by ★ 1.9k • written 2.0 years ago by • 0
0
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3
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1.6k
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Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 2.1 years ago by 16k • written 2.1 years ago by • 0
0
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2
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1.2k
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DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
2.1 years ago • updated 2.0 years ago yr542 • 0
8
votes
7
replies
2.9k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 2.2 years ago by ▴ 20 • written 2.9 years ago by ▴ 20
1
vote
5
replies
1.5k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 2.2 years ago by ★ 1.9k • written 2.2 years ago by • 0
0
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0
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760
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
2.3 years ago nick_brittain55 • 0
0
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0
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686
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Error while performing DEXseq
DEXSeq
2.3 years ago vipul14 • 0
0
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0
replies
704
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
2.5 years ago Ben J ▴ 20
2
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2
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1.7k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.6 years ago Ben J ▴ 20
0
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0
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958
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
votes
1
reply
1.2k
views
plotDEXSeq error?
DEXSeq dex
2.8 years ago barrypraveen • 0
1
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4
replies
1.4k
views
DEXseq batch removal
DEXSeq
updated 2.9 years ago by ★ 1.9k • written 2.9 years ago by ▴ 10
0
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0
replies
694
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
3.0 years ago Matthias Munz ▴ 20
0
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0
replies
779
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.1 years ago osieman52 • 0
1
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2
replies
1.3k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
3.1 years ago Delta._.43 ▴ 20
0
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1
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1.3k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
3.3 years ago NIK • 0
0
votes
4
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2.5k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 3.3 years ago by ▴ 100 • written 3.4 years ago by • 0
0
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5
replies
2.5k
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DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 6.4 years ago by • 0
8
votes
12
replies
4.7k
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 15 months ago by ▴ 30 • written 3.4 years ago by ▴ 380
3
votes
2
replies
1.7k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.4 years ago Dakarai ▴ 10
1
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1
reply
1.0k
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 3.5 years ago by ★ 1.9k • written 3.5 years ago by • 0
1
vote
2
replies
1.4k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.8 years ago • updated 3.6 years ago A ▴ 60
3
votes
3
replies
1.6k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 120
0
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1
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1.3k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 3.6 years ago by ★ 1.9k • written 3.9 years ago by • 0
1
vote
1
reply
1.6k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3.6 years ago by ★ 1.9k • written 4.1 years ago by ▴ 10
2
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7
replies
1.9k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
4.1 years ago • updated 4.0 years ago rbenel ▴ 50
0
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5
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1.9k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
4.1 years ago bioinformatic_trainee ▴ 10
1
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0
replies
1.5k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
4.1 years ago Matthias Munz ▴ 20
0
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0
replies
945
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
4.2 years ago n.tear ▴ 20
0
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0
replies
952
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
4.2 years ago Matthias Munz ▴ 20
1
vote
6
replies
2.2k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 4.3 years ago by ▴ 120 • written 4.4 years ago by ▴ 10
4
votes
5
replies
2.8k
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
4.4 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.3k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
4.4 years ago jbono ▴ 10
0
votes
2
replies
1.5k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
4.5 years ago Gaia • 0
3
votes
2
replies
1.5k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
4.5 years ago Angel ▴ 10
2
votes
2
replies
1.6k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.6 years ago • updated 4.5 years ago n.tear ▴ 20
363 results • Page 1 of 8
Recent ...
Replies
Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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