Showing : DEXSEq • reset
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
8 days ago Matthias Munz ▴ 10
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51
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
21 days ago n.tear ▴ 10
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0
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48
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DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
5 weeks ago Matthias Munz ▴ 10
1
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6
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322
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Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 7 weeks ago by ▴ 100 • written 3 months ago by ▴ 10
4
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5
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256
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DEXSeq: What's the best way to map an exon counting bin, e.g. E002 to exon(s) or position in transcript(s)
DEXSeq
3 months ago Matthias Munz ▴ 10
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0
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101
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Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
4 months ago jbono ▴ 10
0
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2
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164
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DRIMSeq + dmFilter
DEXSeq DRIMSeq
4 months ago Gaia • 0
3
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2
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193
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How to better run DEXSeq with a very large number of samples?
DEXSeq
5 months ago • updated 4 months ago Angel ▴ 10
2
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2
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195
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Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
5 months ago • updated 4 months ago n.tear ▴ 10
1
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1
reply
202
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Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 7 months ago by ★ 1.8k • written 7 months ago by • 0
0
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2
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234
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DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
13 months ago • updated 8 months ago aleksandar.baburski.g • 0
1
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6
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2.5k
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DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 8 months ago by ▴ 10 • written 6.4 years ago by • 0
0
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2
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578
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Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 8 months ago by ▴ 10 • written 3.6 years ago by • 0
5
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7
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474
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Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 7 months ago by 33k • written 9 months ago by ▴ 10
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4
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640
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DEXSeq - counts from paired reads and unpaired singletons
dexseq
updated 9 months ago by • 0 • written 2.3 years ago by • 0
0
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2
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180
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DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 12 months ago by ★ 3.7k • written 12 months ago by • 0
0
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4
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234
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Calculating per-exon PSI from DEXSeq
DEXSeq
12 months ago Angel Liang • 0
1
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2
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173
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Detailed explanations for DEXSeq output columns
DEXSeq
updated 12 months ago by ★ 1.8k • written 12 months ago by • 0
0
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1
reply
130
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 13 months ago by 33k • written 13 months ago by ▴ 10
1
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2
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207
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DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq estimateDispersions
13 months ago aleksandar.baburski.g • 0
0
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2
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197
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DEXSeq HTML report Error
DEXSeq
updated 13 months ago by 3.2k • written 13 months ago by • 0
0
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0
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104
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Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
14 months ago alexis.weinreb • 0
1
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2
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221
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DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq python gtf gff3 annotation
15 months ago Raito92 ▴ 50
0
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1
reply
168
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DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error DEXSeq
15 months ago knuppdav • 0
1
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3
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251
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DEXSeq with large(ish) number of samples
DEXSeq exon memory dispersions estimateDispersions
15 months ago andreismolnikov00 • 0
0
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0
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185
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summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 15 months ago by 25k • written 15 months ago by ▴ 10
0
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2
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209
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 16 months ago by 25k • written 16 months ago by • 0
1
vote
2
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154
views
How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 16 months ago by ★ 1.8k • written 16 months ago by • 0
0
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3
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312
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DEXSeq Splicing Result with incomplete lines between exons
DEXSeq Splicing Exon Usage
18 months ago gunjan.dikshit • 0
2
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6
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440
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featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 20 months ago by ▴ 260 • written 20 months ago by • 0
0
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1
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198
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq splicing RNAseq DEXSeq
20 months ago stuart ▴ 10
0
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1
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182
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error in DEXSeq estimateExonFoldChanges
dexseq
20 months ago brown.annaleigh • 0
0
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2
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271
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A question about DEXSeq of estimateDispersions
dexseq
updated 22 months ago by • 0 • written 23 months ago by • 0
0
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2
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316
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Issue/Error with DEXSeq design formulae in testForDEU function
deseq2 DEXSeq BioCParallel
updated 23 months ago by ★ 1.8k • written 23 months ago by • 0
0
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1
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681
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 2.0 years ago by 57k • written 2.0 years ago by • 0
0
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2
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325
views
DEXSeq error in dexseq_count.py. ValueError: need more than 4 values to unpack
DEXSeq
updated 2.1 years ago by ★ 3.7k • written 2.1 years ago by • 0
2
votes
1
reply
288
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 2.2 years ago by ★ 1.8k • written 2.2 years ago by • 0
2
votes
3
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316
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 2.2 years ago by 15k • written 2.2 years ago by ▴ 10
0
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6
replies
515
views
DEXSeq dispersion outlier
DEXSeq dispersion pvalue
2.3 years ago • updated 2.2 years ago fiona.dick91 ▴ 10
1
vote
3
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361
views
null model and DEXSeqDataSet object in DEXSEQ
deseq2 dexseq
2.2 years ago gv ▴ 40
2
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6
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423
views
estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2 dexseq
2.2 years ago gv ▴ 40
1
vote
6
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444
views
How to install DEXSeq on R 3.4.4
DEXSEq Linux
updated 2.3 years ago by ★ 1.8k • written 2.3 years ago by • 0
1
vote
1
reply
590
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 2.3 years ago by 33k • written 2.6 years ago by ▴ 10
0
votes
11
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552
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Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU DRIMseq DEXseq rna-seq
2.3 years ago saddamhusain77 • 0
0
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2
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303
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DEXSeq With Reduced Annotations
dexseq reduced annotation set
2.4 years ago sumeet460 • 0
1
vote
2
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501
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Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 2.4 years ago by ▴ 80 • written 2.5 years ago by ▴ 20
2
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4
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528
views
stageR: Error in stageWiseAdjustment
stageR rnaseqDTU DRIMSeq DEXSeq
2.5 years ago d-joester ▴ 20
0
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4
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496
views
tximport: Error in medianLengthOverIsoform
tximport deseq2 dexseq
2.5 years ago d-joester ▴ 20
0
votes
1
reply
353
views
DEXSeq: controlling for cell composition
dexseq
updated 2.5 years ago by ★ 1.8k • written 2.6 years ago by • 0
0
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1
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380
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Can DEXseq be used for splicing QTL analysis?
dexseq splicing sqtl qtl
updated 2.5 years ago by ★ 1.8k • written 2.5 years ago by • 0
50 results • Page 1 of 1
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Answer: tximeta countsFromAbundance for downstream analysis by Michael Love 33k
The counts will not be closely correlated to the TPM across genes, because the gene length is included in the gene count but not in the TPM…
Answer: DESeq2 - understanding intercept and contrasts by Michael Love 33k
For questions on setting up the statistical design and contrasts, I recommend to consult with a local statistician or someone familiar with…
Answer: Interaction terms and selection of coef in normal and shrunk results by Michael Love 33k
Please see the diagram in the vignette on interactions, but for further questions on setting up the design, I recommend to consult with a l…
Answer: about baseMean in DEseq2 by Michael Love 33k
More information about the columns is here: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#access-…
Answer: DESeq2, what to do when controls are 7 times more abundant than treatments by Michael Love 33k
I generally recommend your option 2 here: filtering out genes unless they are minimally expressed in the lowly sequenced condition. This is…
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