Showing : DEXseq • reset
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38
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
15 days ago Ben J • 0
6
votes
6
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380
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Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
5 months ago • updated 19 days ago jeremymsimon ▴ 20
0
votes
2
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155
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
7 weeks ago Ben J • 0
0
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0
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157
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DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 3 months ago by 39k • written 4 months ago by • 0
0
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1
reply
221
views
plotDEXSeq error?
DEXSeq dex
4 months ago barrypraveen • 0
1
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4
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384
views
DEXseq batch removal
DEXSeq
updated 5 months ago by ★ 1.8k • written 5 months ago by ▴ 10
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0
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121
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
6 months ago Matthias Munz ▴ 10
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0
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183
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
7 months ago osieman52 • 0
1
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2
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295
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DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
7 months ago Delta._.43 ▴ 20
0
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1
reply
343
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
10 months ago NIK • 0
0
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4
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625
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DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 10 months ago by ▴ 90 • written 11 months ago by • 0
0
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5
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1.3k
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DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 4.0 years ago by • 0
6
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11
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1.3k
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 8 days ago by • 0 • written 11 months ago by ▴ 350
3
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2
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423
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
11 months ago • updated 10 months ago Dakarai ▴ 10
1
vote
1
reply
304
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 12 months ago by ★ 1.8k • written 12 months ago by • 0
1
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2
replies
474
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
16 months ago • updated 14 months ago A ▴ 40
3
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3
replies
519
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 14 months ago by 39k • written 14 months ago by ▴ 120
0
votes
1
reply
429
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 14 months ago by ★ 1.8k • written 17 months ago by • 0
0
votes
1
reply
537
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 14 months ago by ★ 1.8k • written 19 months ago by • 0
2
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7
replies
636
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
19 months ago rbenel ▴ 20
0
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5
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574
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
19 months ago bioinformatic_trainee ▴ 10
0
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0
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378
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
20 months ago Matthias Munz ▴ 10
0
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0
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328
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
20 months ago n.tear ▴ 20
0
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0
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310
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DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
21 months ago Matthias Munz ▴ 10
1
vote
6
replies
902
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 21 months ago by ▴ 120 • written 23 months ago by ▴ 10
4
votes
5
replies
963
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
23 months ago Matthias Munz ▴ 10
0
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0
replies
445
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
24 months ago jbono ▴ 10
0
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2
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521
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
2.0 years ago Gaia • 0
3
votes
2
replies
617
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
2.1 years ago • updated 2.0 years ago Angel ▴ 10
2
votes
2
replies
726
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
2.1 years ago • updated 2.0 years ago n.tear ▴ 20
1
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1
reply
572
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 2.2 years ago by ★ 1.8k • written 2.2 years ago by • 0
0
votes
2
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716
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DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
2.8 years ago • updated 2.4 years ago aleksandar.baburski.g • 0
1
vote
6
replies
3.1k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 2.4 years ago by ▴ 20 • written 8.0 years ago by • 0
0
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2
replies
1.0k
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 2.4 years ago by ▴ 20 • written 5.2 years ago by • 0
6
votes
7
replies
1.1k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 2.3 years ago by 39k • written 2.4 years ago by ▴ 20
0
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2
replies
467
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 2.7 years ago by ★ 3.7k • written 2.7 years ago by • 0
0
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4
replies
856
views
Calculating per-exon PSI from DEXSeq
DEXSeq
2.7 years ago Angel Liang • 0
1
vote
2
replies
651
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 2.7 years ago by ★ 1.8k • written 2.7 years ago by • 0
0
votes
1
reply
409
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 2.7 years ago by 39k • written 2.7 years ago by ▴ 10
1
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2
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700
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq estimateDispersions
2.8 years ago aleksandar.baburski.g • 0
0
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2
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535
views
DEXSeq HTML report Error
DEXSeq
updated 2.8 years ago by 3.8k • written 2.8 years ago by • 0
0
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0
replies
361
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
2.9 years ago alexis.weinreb • 0
1
vote
2
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875
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq python gtf gff3 annotation
2.9 years ago Raito92 ▴ 60
0
votes
1
reply
595
views
DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error DEXSeq
2.9 years ago knuppdav • 0
1
vote
3
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760
views
DEXSeq with large(ish) number of samples
DEXSeq exon memory dispersions estimateDispersions
2.9 years ago andreismolnikov00 • 0
0
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0
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979
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 2.9 years ago by 25k • written 2.9 years ago by ▴ 10
3
votes
3
replies
1.1k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 19 months ago by ▴ 20 • written 3.0 years ago by ▴ 20
1
vote
2
replies
404
views
How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 3.0 years ago by ★ 1.8k • written 3.0 years ago by • 0
0
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3
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684
views
DEXSeq Splicing Result with incomplete lines between exons
DEXSeq Splicing Exon Usage
3.1 years ago gunjan.dikshit • 0
2
votes
6
replies
1.6k
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 3.3 years ago by ▴ 350 • written 3.3 years ago by • 0
50 results • Page 1 of 1
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Comment: Annotated dendogram (tree) from tbl_graph by christian.dina • 0
Hi, I don't see a way delete the messages. I haved moved on this topic and I will issue more precise questions, so just a warning this is d…
Comment: Failed to install Biobase by johann.brisseau • 0
Hi James When i launched the link via browser, i had message from Zcaller which bloked the access here below the message Access to this we…
Comment: how can I do gene differential analysis on data after vst by linouhao ▴ 20
GSE156237_DESeq2_vsd_exp.txt.gz I have a gene expression matrix, the data in it was transformed by vst, how can I do differential analysis…
Comment: how can I do gene differential analysis on data after vst by ATpoint ★ 2.4k
I do not understand what you mean. Please search previous posts. vst can be used with limma, and DESeq2 needs raw counts as described in th…
Comment: how can I do gene differential analysis on data after vst by linouhao ▴ 20
hi thanks a lot. It is a matrix, not much related to GEO, more related to DESEQ2, I want to know if raw count after VST function , then c…
Votes
Answer: HISAT2 mapping
C: biomaRt question for GO term search
A: biomaRt question for GO term search
biomaRt question for GO term search
Answer: Accounting for breadth of coverage while using DESeq2
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