Showing : DEXSeq • reset
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
updated 1 day ago by 13k • written 1 day ago by • 0
0
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0
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120
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 9 weeks ago by 39k • written 9 weeks ago by • 0
0
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0
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100
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Complex experimental design in DEXSEQ & many samples
DEXSeq
10 weeks ago Ben J • 0
0
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1
reply
175
views
plotDEXSeq error?
DEXSeq dex
10 weeks ago • updated 9 weeks ago barrypraveen • 0
0
votes
1
reply
170
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 3 months ago by 39k • written 3 months ago by • 0
1
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4
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319
views
DEXseq batch removal
DEXSeq
updated 3 months ago by ★ 1.8k • written 3 months ago by ▴ 10
0
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0
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99
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
4 months ago Matthias Munz ▴ 10
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0
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147
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
5 months ago osieman52 • 0
1
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2
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244
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
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1
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297
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
8 months ago NIK • 0
0
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4
replies
546
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 8 months ago by ▴ 70 • written 9 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 3.8 years ago by • 0
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 6 weeks ago by • 0 • written 9 months ago by ▴ 350
3
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2
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376
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
10 months ago • updated 9 months ago Dakarai ▴ 10
1
vote
1
reply
274
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
429
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
14 months ago • updated 12 months ago A ▴ 40
3
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3
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464
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 12 months ago by 39k • written 12 months ago by ▴ 120
0
votes
1
reply
392
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
0
votes
1
reply
483
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
2
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7
replies
575
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
17 months ago rbenel ▴ 20
0
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5
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513
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
18 months ago • updated 17 months ago bioinformatic_trainee ▴ 10
0
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0
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344
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
18 months ago Matthias Munz ▴ 10
0
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0
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303
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
19 months ago n.tear ▴ 20
0
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0
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287
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
19 months ago Matthias Munz ▴ 10
1
vote
6
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843
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 19 months ago by ▴ 120 • written 22 months ago by ▴ 10
4
votes
5
replies
893
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
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0
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406
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
22 months ago jbono ▴ 10
0
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2
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484
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
22 months ago Gaia • 0
3
votes
2
replies
570
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
23 months ago Angel ▴ 10
2
votes
2
replies
676
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
23 months ago n.tear ▴ 20
1
vote
1
reply
531
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
0
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2
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655
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
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6
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3.0k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 2.2 years ago by ▴ 20 • written 7.9 years ago by • 0
0
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2
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980
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Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 2.2 years ago by ▴ 20 • written 5.1 years ago by • 0
6
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7
replies
993
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 2.1 years ago by 39k • written 2.2 years ago by ▴ 20
0
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2
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423
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 2.6 years ago by • 0
0
votes
4
replies
786
views
Calculating per-exon PSI from DEXSeq
DEXSeq
2.5 years ago Angel Liang • 0
1
vote
2
replies
599
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 2.6 years ago by ★ 1.8k • written 2.6 years ago by • 0
0
votes
1
reply
379
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
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637
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq estimateDispersions
2.6 years ago aleksandar.baburski.g • 0
0
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2
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505
views
DEXSeq HTML report Error
DEXSeq
updated 2.6 years ago by 3.7k • written 2.6 years ago by • 0
0
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0
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326
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
2.7 years ago alexis.weinreb • 0
1
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2
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804
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq python gtf gff3 annotation
2.8 years ago • updated 2.7 years ago Raito92 ▴ 60
0
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1
reply
560
views
DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error DEXSeq
2.8 years ago knuppdav • 0
1
vote
3
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710
views
DEXSeq with large(ish) number of samples
DEXSeq exon memory dispersions estimateDispersions
2.8 years ago andreismolnikov00 • 0
0
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0
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912
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
3
votes
3
replies
977
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 17 months ago by ▴ 20 • written 2.8 years ago by ▴ 20
1
vote
2
replies
376
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
0
votes
3
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643
views
DEXSeq Splicing Result with incomplete lines between exons
DEXSeq Splicing Exon Usage
3.0 years ago gunjan.dikshit • 0
2
votes
6
replies
1.4k
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 3.2 years ago by ▴ 350 • written 3.2 years ago by • 0
50 results • Page 1 of 1
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Comment: mas5calls function doesn't work; mirna40cdf problem by Berna • 0
Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?
Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage by ayabalbaa1990 • 0
Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…
Comment: Combat and dds Object by shaimaa • 0
I used the combat-seq but the deseq complain as its not integer what should i do
Answer: Different summary() and results() values in DeSeq2 by Basti ▴ 540
summary() tells you the number of genes with low counts, see independant filtering of results in the DESeq2 vignette : https://www.biocondu…
Comment: Atena package - error (new user) by beatriz.calvo ▴ 30
Hi Lalani, We have fixed the bug that lead to the error. The new version of the package (with the bug fixed) will be available in 24-48h. …
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
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