Showing : Dexseq • reset
5
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10
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1.1k
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 weeks ago by • 0 • written 9 months ago by ▴ 350
1
vote
15
replies
2.3k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 5 weeks ago by • 0 • written 5.8 years ago by • 0
0
votes
0
replies
112
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 8 weeks ago by 39k • written 8 weeks ago by • 0
0
votes
1
reply
170
views
plotDEXSeq error?
DEXSeq dex
9 weeks ago • updated 8 weeks ago barrypraveen • 0
0
votes
0
replies
93
views
Complex experimental design in DEXSEQ & many samples
DEXSeq
9 weeks ago Ben J • 0
0
votes
1
reply
160
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 3 months ago by 39k • written 3 months ago by • 0
1
vote
4
replies
311
views
DEXseq batch removal
DEXSeq
updated 3 months ago by ★ 1.8k • written 3 months ago by ▴ 10
0
votes
0
replies
94
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
4 months ago Matthias Munz ▴ 10
1
vote
2
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1.4k
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 5 months ago by ▴ 10 • written 3.5 years ago by ▴ 10
0
votes
0
replies
138
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
5 months ago osieman52 • 0
1
vote
2
replies
240
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
5 months ago Delta._.43 ▴ 20
0
votes
1
reply
289
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
8 months ago NIK • 0
0
votes
4
replies
527
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 8 months ago by ▴ 70 • written 8 months ago by • 0
3
votes
2
replies
372
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
9 months ago • updated 8 months ago Dakarai ▴ 10
0
votes
5
replies
1.3k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 3.8 years ago by • 0
1
vote
1
reply
270
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 10 months ago by ★ 1.8k • written 10 months ago by • 0
1
vote
2
replies
423
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
14 months ago • updated 12 months ago A ▴ 40
0
votes
1
reply
473
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 12 months ago by ★ 1.8k • written 17 months ago by • 0
0
votes
1
reply
385
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 12 months ago by ★ 1.8k • written 15 months ago by • 0
3
votes
3
replies
461
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 12 months ago by 39k • written 12 months ago by ▴ 120
3
votes
2
replies
1.3k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq fit matrix warning
updated 14 months ago by • 0 • written 6.0 years ago by ★ 1.5k
2
votes
7
replies
569
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
17 months ago • updated 16 months ago rbenel ▴ 20
3
votes
3
replies
967
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 17 months ago by ▴ 20 • written 2.8 years ago by ▴ 20
0
votes
5
replies
499
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
17 months ago bioinformatic_trainee ▴ 10
0
votes
0
replies
340
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
18 months ago Matthias Munz ▴ 10
0
votes
0
replies
297
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
18 months ago n.tear ▴ 20
0
votes
0
replies
285
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
19 months ago Matthias Munz ▴ 10
1
vote
6
replies
836
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 19 months ago by ▴ 120 • written 21 months ago by ▴ 10
4
votes
5
replies
879
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
21 months ago Matthias Munz ▴ 10
0
votes
0
replies
401
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
22 months ago jbono ▴ 10
0
votes
2
replies
478
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
22 months ago Gaia • 0
2
votes
2
replies
668
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
23 months ago • updated 22 months ago n.tear ▴ 20
3
votes
2
replies
565
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
23 months ago • updated 22 months ago Angel ▴ 10
1
vote
1
reply
523
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 2.1 years ago by ★ 1.8k • written 2.1 years ago by • 0
6
votes
7
replies
978
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 2.1 years ago by 39k • written 2.2 years ago by ▴ 20
0
votes
2
replies
649
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
2.6 years ago • updated 2.2 years ago aleksandar.baburski.g • 0
1
vote
6
replies
3.0k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 2.2 years ago by ▴ 20 • written 7.8 years ago by • 0
0
votes
2
replies
975
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 2.2 years ago by ▴ 20 • written 5.1 years ago by • 0
0
votes
2
replies
419
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 2.5 years ago by ★ 3.7k • written 2.5 years ago by • 0
0
votes
4
replies
778
views
Calculating per-exon PSI from DEXSeq
DEXSeq
2.5 years ago Angel Liang • 0
1
vote
2
replies
594
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 2.5 years ago by ★ 1.8k • written 2.5 years ago by • 0
0
votes
1
reply
374
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 2.6 years ago by 39k • written 2.6 years ago by ▴ 10
1
vote
2
replies
633
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq estimateDispersions
2.6 years ago aleksandar.baburski.g • 0
0
votes
2
replies
501
views
DEXSeq HTML report Error
DEXSeq
updated 2.6 years ago by 3.7k • written 2.6 years ago by • 0
0
votes
0
replies
322
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
2.7 years ago alexis.weinreb • 0
1
vote
2
replies
794
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq python gtf gff3 annotation
2.7 years ago Raito92 ▴ 60
0
votes
1
reply
555
views
DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error DEXSeq
2.7 years ago knuppdav • 0
1
vote
3
replies
703
views
DEXSeq with large(ish) number of samples
DEXSeq exon memory dispersions estimateDispersions
2.8 years ago andreismolnikov00 • 0
0
votes
0
replies
905
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 2.8 years ago by 25k • written 2.8 years ago by ▴ 10
1
vote
2
replies
370
views
How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 2.8 years ago by ★ 1.8k • written 2.8 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
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