Showing : DEXSeq • reset
2
votes
3
replies
116
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Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 8 days ago by 35k • written 9 days ago by ▴ 100
0
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0
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96
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Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
8 weeks ago A ▴ 40
0
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0
replies
128
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DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
3 months ago Hahsooni • 0
0
votes
0
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120
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DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
5 months ago • updated 4 months ago Nirad • 0
2
votes
7
replies
292
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
5 months ago • updated 4 months ago rbenel ▴ 20
0
votes
5
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206
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
5 months ago bioinformatic_trainee • 0
0
votes
0
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135
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
5 months ago Matthias Munz ▴ 10
0
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0
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143
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
6 months ago n.tear ▴ 20
0
votes
0
replies
123
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
7 months ago Matthias Munz ▴ 10
1
vote
6
replies
524
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 7 months ago by ▴ 100 • written 9 months ago by ▴ 10
4
votes
5
replies
450
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
8 months ago Matthias Munz ▴ 10
0
votes
0
replies
195
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
9 months ago jbono ▴ 10
0
votes
2
replies
269
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
10 months ago Gaia • 0
3
votes
2
replies
332
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
10 months ago Angel ▴ 10
2
votes
2
replies
358
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
11 months ago • updated 10 months ago n.tear ▴ 20
1
vote
1
reply
320
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 12 months ago by ★ 1.8k • written 12 months ago by • 0
0
votes
2
replies
381
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
19 months ago • updated 14 months ago aleksandar.baburski.g • 0
1
vote
6
replies
2.7k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 14 months ago by ▴ 20 • written 6.8 years ago by • 0
0
votes
2
replies
703
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 14 months ago by ▴ 20 • written 4.1 years ago by • 0
6
votes
7
replies
662
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 13 months ago by 35k • written 14 months ago by ▴ 20
0
votes
4
replies
840
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
updated 14 months ago by • 0 • written 2.8 years ago by • 0
0
votes
2
replies
261
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 18 months ago by ★ 3.7k • written 18 months ago by • 0
0
votes
4
replies
412
views
Calculating per-exon PSI from DEXSeq
DEXSeq
18 months ago Angel Liang • 0
1
vote
2
replies
292
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 18 months ago by ★ 1.8k • written 18 months ago by • 0
0
votes
1
reply
216
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 19 months ago by 35k • written 19 months ago by ▴ 10
1
vote
2
replies
359
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq estimateDispersions
19 months ago aleksandar.baburski.g • 0
0
votes
2
replies
298
views
DEXSeq HTML report Error
DEXSeq
updated 19 months ago by 3.4k • written 19 months ago by • 0
0
votes
0
replies
175
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
20 months ago alexis.weinreb • 0
1
vote
2
replies
364
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq python gtf gff3 annotation
21 months ago • updated 20 months ago Raito92 ▴ 50
0
votes
1
reply
262
views
DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error DEXSeq
21 months ago knuppdav • 0
1
vote
3
replies
378
views
DEXSeq with large(ish) number of samples
DEXSeq exon memory dispersions estimateDispersions
21 months ago andreismolnikov00 • 0
0
votes
0
replies
398
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 21 months ago by 25k • written 21 months ago by ▴ 10
3
votes
3
replies
431
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 4 months ago by ▴ 20 • written 21 months ago by ▴ 20
1
vote
2
replies
234
views
How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 21 months ago by ★ 1.8k • written 22 months ago by • 0
0
votes
3
replies
432
views
DEXSeq Splicing Result with incomplete lines between exons
DEXSeq Splicing Exon Usage
23 months ago gunjan.dikshit • 0
2
votes
6
replies
719
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 2.1 years ago by ▴ 290 • written 2.1 years ago by • 0
0
votes
1
reply
288
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq splicing RNAseq DEXSeq
2.1 years ago stuart ▴ 10
0
votes
1
reply
250
views
error in DEXSeq estimateExonFoldChanges
dexseq
2.2 years ago brown.annaleigh • 0
0
votes
2
replies
350
views
A question about DEXSeq of estimateDispersions
dexseq
updated 2.3 years ago by • 0 • written 2.4 years ago by • 0
0
votes
2
replies
424
views
Issue/Error with DEXSeq design formulae in testForDEU function
deseq2 DEXSeq BioCParallel
updated 2.4 years ago by ★ 1.8k • written 2.4 years ago by • 0
0
votes
1
reply
934
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 2.5 years ago by 58k • written 2.5 years ago by • 0
0
votes
2
replies
417
views
DEXSeq error in dexseq_count.py. ValueError: need more than 4 values to unpack
DEXSeq
updated 2.6 years ago by ★ 3.7k • written 2.6 years ago by • 0
2
votes
1
reply
362
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 2.6 years ago by ★ 1.8k • written 2.6 years ago by • 0
2
votes
3
replies
417
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 2.7 years ago by 15k • written 2.7 years ago by ▴ 10
0
votes
6
replies
658
views
DEXSeq dispersion outlier
DEXSeq dispersion pvalue
2.7 years ago fiona.dick91 ▴ 10
1
vote
3
replies
526
views
null model and DEXSeqDataSet object in DEXSEQ
deseq2 dexseq
2.7 years ago gv ▴ 40
2
votes
6
replies
556
views
estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2 dexseq
2.7 years ago gv ▴ 40
1
vote
6
replies
602
views
How to install DEXSeq on R 3.4.4
DEXSEq Linux
updated 2.7 years ago by ★ 1.8k • written 2.7 years ago by • 0
1
vote
1
reply
702
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 2.7 years ago by 35k • written 3.0 years ago by ▴ 10
0
votes
11
replies
821
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU DRIMseq DEXseq rna-seq
2.8 years ago saddamhusain77 • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Need help for ProStaR Stand-alone install by benoit.marchand • 0
Thank you for answering. I've just updated to Prostar v1.26.3 and confirm that the **Prostar()** command **now works** in R for me on linu…
Answer: airway package not compatible with R version 4.1.2 (2021-11-01) by ATpoint ▴ 970
`data(airway)` is your friend. The CRAN error comes from the fact that it is not a CRAN package, not that it is a version problem itself.
Comment: airway package not compatible with R version 4.1.2 (2021-11-01) by Lluís Revilla Sancho ▴ 660
I think it would help if you try again to install it via `BiocManager::install("airway")` and report the exact text output (without quittin…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by Michael Love 35k
This looks as expected with the control genes centered on the x-axis (yes, these can have high variance, this is discussed in work by Risso…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by argonvibio • 0
Hello Michael, and thank you for your reply. I have done as you described, estimating size factors with controlGenes before DESeq, but the…
Votes
Comment: Need help for ProStaR Stand-alone install
Emirical Bayesian shrinkage for dispertion/LFC estimation
C: Emirical Bayesian shrinkage for dispertion/LFC estimation
A: Emirical Bayesian shrinkage for dispertion/LFC estimation
Comment: airway package not compatible with R version 4.1.2 (2021-11-01)
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