Showing : DEXseq • reset
0
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263
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Make DEXSeq plot normal scale
DEXSeq Dexseq
updated 6 months ago by 68k • written 6 months ago by • 0
4
votes
6
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1.5k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
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0
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318
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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
8 months ago cftattersfield • 0
0
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1
reply
533
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
2
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1
reply
760
views
How to design DEXSeq formula for multiple variables
DEXSeq
17 months ago • updated 16 months ago Sara • 0
3
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1
reply
846
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How to save the DEXSeq results
DEXSeq
updated 17 months ago by 43k • written 17 months ago by • 0
0
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0
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501
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
18 months ago Sara • 0
0
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3
replies
820
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 18 months ago by ★ 1.9k • written 18 months ago by • 0
0
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1
reply
627
views
Adding columns to DEXSeqResults object
DEXSeq
updated 18 months ago by ★ 1.9k • written 18 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 18 months ago by 43k • written 18 months ago by • 0
0
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0
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470
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
19 months ago jean-christophe.helbling • 0
2
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4
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1.1k
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
21 months ago • updated 20 months ago thomas.heigl.ibk • 0
0
votes
2
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830
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Swimming downstream: transcript fold changes
DEXSeq stageR
23 months ago jbono ▴ 10
1
vote
1
reply
911
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
24 months ago NiKo ▴ 10
0
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3
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1.3k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 2.2 years ago by ★ 1.9k • written 2.2 years ago by • 0
0
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3
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1.6k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 2.2 years ago by 16k • written 2.3 years ago by • 0
0
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2
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1.2k
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
2.2 years ago • updated 2.1 years ago yr542 • 0
8
votes
7
replies
3.0k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 2.3 years ago by ▴ 20 • written 3.0 years ago by ▴ 20
1
vote
5
replies
1.5k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by • 0
0
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0
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784
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
2.4 years ago nick_brittain55 • 0
0
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0
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700
views
Error while performing DEXseq
DEXSeq
2.4 years ago vipul14 • 0
0
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0
replies
725
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
2.6 years ago Ben J ▴ 20
2
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2
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1.8k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.7 years ago Ben J ▴ 20
0
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0
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977
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
1
reply
1.2k
views
plotDEXSeq error?
DEXSeq dex
2.9 years ago barrypraveen • 0
1
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4
replies
1.5k
views
DEXseq batch removal
DEXSeq
updated 3.0 years ago by ★ 1.9k • written 3.0 years ago by ▴ 10
0
votes
0
replies
708
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
3.1 years ago Matthias Munz ▴ 20
0
votes
0
replies
804
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.2 years ago osieman52 • 0
1
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2
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1.4k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
3.2 years ago Delta._.43 ▴ 20
0
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1
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1.4k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
3.4 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 3.4 years ago by ▴ 100 • written 3.5 years ago by • 0
0
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5
replies
2.6k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 6.5 years ago by • 0
8
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12
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4.8k
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 17 months ago by ▴ 30 • written 3.5 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
3.6 years ago • updated 3.5 years ago Dakarai ▴ 10
1
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1
reply
1.1k
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 3.6 years ago by ★ 1.9k • written 3.6 years ago by • 0
1
vote
2
replies
1.5k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.9 years ago • updated 3.7 years ago A ▴ 60
3
votes
3
replies
1.6k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 120
0
votes
1
reply
1.3k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 3.8 years ago by ★ 1.9k • written 4.0 years ago by • 0
1
vote
1
reply
1.7k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3.8 years ago by ★ 1.9k • written 4.2 years ago by ▴ 10
2
votes
7
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2.0k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
4.2 years ago • updated 4.1 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
4.2 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
4.2 years ago Matthias Munz ▴ 20
0
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0
replies
960
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
4.3 years ago n.tear ▴ 20
0
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0
replies
970
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
4.3 years ago Matthias Munz ▴ 20
1
vote
6
replies
2.3k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 4.4 years ago by ▴ 120 • written 4.5 years ago by ▴ 10
4
votes
5
replies
2.9k
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
4.5 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.3k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
4.6 years ago jbono ▴ 10
0
votes
2
replies
1.5k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
4.6 years ago Gaia • 0
3
votes
2
replies
1.5k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
4.6 years ago Angel ▴ 10
2
votes
2
replies
1.7k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.7 years ago • updated 4.6 years ago n.tear ▴ 20
363 results • Page 1 of 8
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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