Showing : DEXSeq • reset
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2 hours ago Matthias Munz ▴ 10
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0
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44
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
13 days ago n.tear ▴ 10
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0
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46
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DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
4 weeks ago Matthias Munz ▴ 10
1
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6
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312
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Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 5 weeks ago by ▴ 100 • written 3 months ago by ▴ 10
4
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5
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242
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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
12 weeks ago • updated 11 weeks ago Matthias Munz ▴ 10
0
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0
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98
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Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3 months ago jbono ▴ 10
0
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2
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156
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DRIMSeq + dmFilter
DEXSeq DRIMSeq
4 months ago Gaia • 0
3
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2
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189
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How to better run DEXSeq with a very large number of samples?
DEXSeq
4 months ago Angel ▴ 10
2
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2
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187
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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
vote
1
reply
185
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Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 6 months ago by ★ 1.8k • written 6 months ago by • 0
0
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2
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231
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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 6.3 years ago by • 0
0
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2
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572
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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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466
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Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 7 months ago by 33k • written 8 months ago by ▴ 10
0
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4
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631
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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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170
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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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225
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Calculating per-exon PSI from DEXSeq
DEXSeq
12 months ago Angel Liang • 0
1
vote
2
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167
views
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
124
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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202
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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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191
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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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98
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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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215
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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 • updated 14 months ago Raito92 ▴ 50
0
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1
reply
160
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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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240
views
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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183
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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
replies
199
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 15 months ago by 25k • written 15 months ago by • 0
1
vote
2
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151
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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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303
views
DEXSeq Splicing Result with incomplete lines between exons
DEXSeq Splicing Exon Usage
17 months ago gunjan.dikshit • 0
2
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6
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421
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 19 months ago by ▴ 260 • written 20 months ago by • 0
0
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1
reply
194
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
reply
178
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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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267
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A question about DEXSeq of estimateDispersions
dexseq
updated 21 months ago by • 0 • written 23 months ago by • 0
0
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2
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308
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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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669
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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318
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
284
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 2.1 years ago by ★ 1.8k • written 2.1 years ago by • 0
2
votes
3
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307
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
votes
6
replies
506
views
DEXSeq dispersion outlier
DEXSeq dispersion pvalue
2.2 years ago fiona.dick91 ▴ 10
1
vote
3
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347
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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416
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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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436
views
How to install DEXSeq on R 3.4.4
DEXSEq Linux
updated 2.2 years ago by ★ 1.8k • written 2.2 years ago by • 0
1
vote
1
reply
582
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 2.2 years ago by 33k • written 2.5 years ago by ▴ 10
0
votes
11
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531
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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
votes
2
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297
views
DEXSeq With Reduced Annotations
dexseq reduced annotation set
2.4 years ago sumeet460 • 0
1
vote
2
replies
491
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 2.4 years ago by ▴ 80 • written 2.4 years ago by ▴ 20
2
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4
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514
views
stageR: Error in stageWiseAdjustment
stageR rnaseqDTU DRIMSeq DEXSeq
2.5 years ago d-joester ▴ 20
0
votes
4
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490
views
tximport: Error in medianLengthOverIsoform
tximport deseq2 dexseq
2.5 years ago d-joester ▴ 20
0
votes
1
reply
347
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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376
views
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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Comment: cannot install edgeR on M1 Mac by noname88 • 0
Hi--I recommend seeing the suggestions in response to this post. It solved ALL of my problems with this type of installation! https://sta…
Comment: Using R BioMart getting orthologus genes between two species by Kevin Blighe 3.2k
Then, I think that *biomaRt* may not be what you want, but you tagged it in your post (?) Take a look at the Ensembl REST APIs (in particul…
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Unfortunately, I have to save my time to address software related questions. For questions about how to set up your statistical analysis, I…
Comment: Deseq paired samples by Michael Love 33k
Oh if you are interested in comparing FUS vs NEG in the above sample order, you should define `replicate` as `factor(c(1,2,1,2,3,4,3,4))` a…
Answer: [DESeq2] Question regarding experiment design with multiple nesting and variable by Michael Love 33k
*"I would like to compare the different "cell types" against each other while taking into account the "patient" and the "disease" effect."*…
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Answer: cannot install edgeR on M1 Mac
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