Showing : DEXseq • reset
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35
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
7 days ago Ben J • 0
5
votes
6
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355
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Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
4 months ago • updated 11 days ago jeremymsimon ▴ 10
0
votes
2
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148
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
6 weeks ago Ben J • 0
0
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0
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149
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DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 3 months ago by 39k • written 3 months ago by • 0
0
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1
reply
211
views
plotDEXSeq error?
DEXSeq dex
4 months ago • updated 3 months ago barrypraveen • 0
1
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4
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378
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DEXseq batch removal
DEXSeq
updated 5 months ago by ★ 1.8k • written 5 months ago by ▴ 10
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0
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120
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
6 months ago Matthias Munz ▴ 10
0
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0
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181
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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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290
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
7 months ago Delta._.43 ▴ 20
0
votes
1
reply
339
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DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
10 months ago • updated 9 months ago NIK • 0
0
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4
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619
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DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 9 months ago by ▴ 90 • written 10 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 3.9 years ago by • 0
6
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11
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1.3k
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DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq)
DEXSeq
updated 20 hours ago by • 0 • written 11 months ago by ▴ 350
3
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2
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421
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
301
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 12 months ago by ★ 1.8k • written 12 months ago by • 0
1
vote
2
replies
471
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
16 months ago • updated 13 months ago A ▴ 40
3
votes
3
replies
510
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
427
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
531
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
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630
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
19 months ago • updated 18 months ago rbenel ▴ 20
0
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5
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570
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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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375
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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327
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
replies
305
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
21 months ago Matthias Munz ▴ 10
1
vote
6
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899
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
956
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
22 months ago Matthias Munz ▴ 10
0
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0
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440
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
23 months ago jbono ▴ 10
0
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2
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519
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
2.0 years ago • updated 24 months ago Gaia • 0
3
votes
2
replies
615
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
2.0 years ago Angel ▴ 10
2
votes
2
replies
718
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
vote
1
reply
565
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
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2
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714
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
2.7 years ago • updated 2.3 years ago aleksandar.baburski.g • 0
1
vote
6
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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
votes
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 2.2 years ago by 39k • written 2.4 years ago by ▴ 20
0
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2
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463
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
votes
4
replies
840
views
Calculating per-exon PSI from DEXSeq
DEXSeq
2.7 years ago Angel Liang • 0
1
vote
2
replies
644
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
407
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
vote
2
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692
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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531
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
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359
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
2.8 years ago alexis.weinreb • 0
1
vote
2
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872
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
591
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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755
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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970
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
1.0k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 18 months ago by ▴ 20 • written 3.0 years ago by ▴ 20
1
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2
replies
402
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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
replies
679
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: Does DiffBind make consensus peaks sets for samples from a given condition (e.g. by tahir.msajid • 0
Hi Rory, I came up with another question while analyzing my data. A scenario of analysis: Path to bam files, path to peaks files (broad pe…
Comment: How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_R by Yang Shi ▴ 10
Thanks for your reply sir! Here is the data ([EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv][1]). And there is the data process…
Comment: TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from va by davidhillis • 0
Thank you!
Comment: Time-course, comparison of two groups by boczniak767 ▴ 720
Thank you Gordon for your time and patience, I'd try to be more specific. I've read carefully the three first chapters of `edgeR` user guid…
Comment: TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from va by James W. MacDonald 62k
This works for me. ``` > library(VariantAnnotation) > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGe…
Votes
Comment: TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from va
A: Pathway analysis of differentially methylated CpGs
Comment: TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from va
Comment: TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from va
Answer: TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from va
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