Showing : dexseq • reset
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64
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DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
4 weeks ago Nirad • 0
2
votes
7
replies
191
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
4 weeks ago • updated 20 days ago rbenel ▴ 20
0
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5
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123
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
6 weeks ago greta • 0
0
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0
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77
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
8 weeks ago Matthias Munz ▴ 10
0
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0
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90
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
10 weeks ago n.tear ▴ 10
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0
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77
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DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3 months ago Matthias Munz ▴ 10
1
vote
6
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395
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Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3 months ago by ▴ 100 • written 5 months ago by ▴ 10
4
votes
5
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311
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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
4 months ago Matthias Munz ▴ 10
0
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0
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129
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Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
5 months ago jbono ▴ 10
0
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2
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199
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DRIMSeq + dmFilter
DEXSeq DRIMSeq
6 months ago Gaia • 0
3
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2
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235
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How to better run DEXSeq with a very large number of samples?
DEXSeq
6 months ago Angel ▴ 10
2
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2
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252
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Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
7 months ago • updated 6 months ago n.tear ▴ 10
1
vote
1
reply
245
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 8 months ago by ★ 1.8k • written 8 months ago by • 0
0
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2
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285
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DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
15 months ago • updated 10 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 10 months ago by ▴ 20 • written 6.5 years ago by • 0
0
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2
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619
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Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 10 months ago by ▴ 20 • written 3.7 years ago by • 0
6
votes
7
replies
537
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 9 months ago by 34k • written 10 months ago by ▴ 20
0
votes
4
replies
699
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
updated 11 months ago by • 0 • written 2.5 years ago by • 0
0
votes
2
replies
213
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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 14 months ago by ★ 3.7k • written 14 months ago by • 0
0
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4
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300
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Calculating per-exon PSI from DEXSeq
DEXSeq
14 months ago Angel Liang • 0
1
vote
2
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207
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 14 months ago by ★ 1.8k • written 14 months ago by • 0
0
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1
reply
161
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 15 months ago by 34k • written 15 months ago by ▴ 10
1
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2
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254
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DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq estimateDispersions
15 months ago aleksandar.baburski.g • 0
0
votes
2
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232
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DEXSeq HTML report Error
DEXSeq
updated 15 months ago by 3.4k • written 15 months ago by • 0
0
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0
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134
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Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
16 months ago alexis.weinreb • 0
1
vote
2
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267
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq python gtf gff3 annotation
17 months ago • updated 16 months ago Raito92 ▴ 50
0
votes
1
reply
201
views
DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error DEXSeq
17 months ago knuppdav • 0
1
vote
3
replies
291
views
DEXSeq with large(ish) number of samples
DEXSeq exon memory dispersions estimateDispersions
17 months ago andreismolnikov00 • 0
0
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0
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227
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 17 months ago by 25k • written 17 months ago by ▴ 10
3
votes
3
replies
317
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 25 days ago by ▴ 20 • written 18 months ago by ▴ 20
1
vote
2
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184
views
How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 18 months ago by ★ 1.8k • written 18 months ago by • 0
0
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3
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356
views
DEXSeq Splicing Result with incomplete lines between exons
DEXSeq Splicing Exon Usage
19 months ago gunjan.dikshit • 0
2
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6
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523
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 22 months ago by ▴ 260 • written 22 months ago by • 0
0
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1
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230
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JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq splicing RNAseq DEXSeq
22 months ago stuart ▴ 10
0
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1
reply
208
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error in DEXSeq estimateExonFoldChanges
dexseq
22 months ago brown.annaleigh • 0
0
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2
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297
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A question about DEXSeq of estimateDispersions
dexseq
updated 24 months ago by • 0 • written 2.1 years ago by • 0
0
votes
2
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346
views
Issue/Error with DEXSeq design formulae in testForDEU function
deseq2 DEXSeq BioCParallel
updated 2.1 years ago by ★ 1.8k • written 2.1 years ago by • 0
0
votes
1
reply
746
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 2.2 years ago by 58k • written 2.2 years ago by • 0
0
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2
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352
views
DEXSeq error in dexseq_count.py. ValueError: need more than 4 values to unpack
DEXSeq
updated 2.2 years ago by ★ 3.7k • written 2.3 years ago by • 0
2
votes
1
reply
315
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 2.3 years ago by ★ 1.8k • written 2.3 years ago by • 0
2
votes
3
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348
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 2.3 years ago by 15k • written 2.3 years ago by ▴ 10
0
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6
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567
views
DEXSeq dispersion outlier
DEXSeq dispersion pvalue
2.4 years ago fiona.dick91 ▴ 10
1
vote
3
replies
439
views
null model and DEXSeqDataSet object in DEXSEQ
deseq2 dexseq
2.4 years ago gv ▴ 40
2
votes
6
replies
464
views
estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2 dexseq
2.4 years ago gv ▴ 40
1
vote
6
replies
490
views
How to install DEXSeq on R 3.4.4
DEXSEq Linux
updated 2.4 years ago by ★ 1.8k • written 2.4 years ago by • 0
1
vote
1
reply
638
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 2.4 years ago by 34k • written 2.7 years ago by ▴ 10
0
votes
11
replies
627
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU DRIMseq DEXseq rna-seq
2.5 years ago saddamhusain77 • 0
0
votes
2
replies
337
views
DEXSeq With Reduced Annotations
dexseq reduced annotation set
2.5 years ago sumeet460 • 0
1
vote
2
replies
550
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 2.6 years ago by ▴ 90 • written 2.6 years ago by ▴ 20
2
votes
4
replies
583
views
stageR: Error in stageWiseAdjustment
stageR rnaseqDTU DRIMSeq DEXSeq
2.7 years ago d-joester ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dat by IIart.hubII • 0
What is "coad_clear" in this case? What data have you allotted to it? Can you please share the whole code? Or can anyone answer this questi…
Comment: GenomicScores package: availableGScores and getGScores functions not working by Robert Castelo ★ 2.7k
hi, Indeed you were using an outdated version of the package. Regarding how to install current release version, please read first carefull…
Answer: Unable to install Bioconductor packages by shepherl 2.8k
This normally occurs when R was installed with a different account or an admin account. Unless on this account you won't be able to update…
Comment: GenomicScores package: availableGScores and getGScores functions not working by nattzy94 • 0
I tried to install the latest version of GenomicScores (2.4.0) by downloading the tar.gz and running `install.packages('GenomicScores_2.4.0…
Comment: GenomicScores package: availableGScores and getGScores functions not working by nattzy94 • 0
Thanks for the quick response. Below is my sessionInfo R version 3.6.2 (2019-12-12) Platform: x86_64-apple-darwin15.6.0 (64-bit) …
Votes
A: Differential expression analysis starting from TPM data
Comment: deseq2 machine sizing best practices for very large data set
Comment: Extracting normalized counts in MEDIPS
Comment: "full model matrix is less than full rank"
A: Extracting normalized counts in MEDIPS
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