Showing : dexseq • reset
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
1 day ago Matthias Munz ▴ 10
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46
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
14 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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314
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Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 6 weeks ago by ▴ 100 • written 3 months ago by ▴ 10
4
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5
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252
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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 Matthias Munz ▴ 10
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0
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99
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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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157
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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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189
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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
189
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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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232
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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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573
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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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467
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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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632
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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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172
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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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228
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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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167
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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
124
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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
vote
2
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205
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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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192
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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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101
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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
161
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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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242
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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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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
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202
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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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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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307
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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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425
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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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195
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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268
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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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310
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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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672
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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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320
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
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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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310
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
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510
views
DEXSeq dispersion outlier
DEXSeq dispersion pvalue
2.2 years ago fiona.dick91 ▴ 10
1
vote
3
replies
352
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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418
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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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440
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
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585
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 2.3 years ago by 33k • written 2.5 years ago by ▴ 10
0
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11
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537
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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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298
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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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496
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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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515
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
349
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
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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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Comment: Best practice for quantifying sncRNA by Abhishek • 0
I wonder what would be a good metric to assess the quantification quality
Comment: Best practice for quantifying sncRNA by Abhishek • 0
Thank you for sharing your thoughts. I used Salmon and indexed using hg38 gencodes transcriptome. After the tximport step, I ended up gett…
Comment: DESeq2 question: why I got discrepancy results for DEGs when using different way by Ming ▴ 350
Thx so much for the diagnosis and advice. Indeed, in my data, some genes have all 0 for all sampes of a contrast for both "Mut" and "WT" gr…
Comment: Best practice for quantifying sncRNA by Steve Lianoglou 13k
> It's my opinion that miRNA is a mirage intended to make MDs salivate and biostatisticians wail in misery, but what do I know? I'll tell …
Comment: Idea: Using DESeq2 to test a change in ratio of two genes by Michael Love 33k
Yes, it's true that we take the reference gene(s) as a noise free measurement of the reference variation with this approach, and control ag…
Votes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Answer: Time series DE gene analysis with edgeR where specific timepoints have NA levels
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