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dexseq
•
reset
0
votes
0
replies
22
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
5 days ago
osieman52
• 0
1
vote
2
replies
86
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
6 days ago
Delta._.43
▴ 20
0
votes
1
reply
169
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
12 weeks ago • updated 11 weeks ago
NIK
• 0
0
votes
4
replies
294
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 11 weeks ago by
jeroen.gilis
▴ 70 • written 3 months ago by
phoebe1354
• 0
0
votes
5
replies
1.1k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 3.4 years ago by
maslane
• 0
4
votes
9
replies
525
views
DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq)
DEXSeq
4 months ago • updated 3 months ago
Matthew Thornton
▴ 350
3
votes
2
replies
218
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
4 months ago • updated 3 months ago
Dakarai
▴ 10
1
vote
1
reply
167
views
Increased number of exons in DEXSeq
DEXSeq
exon
updated 4 months ago by
Alejandro Reyes
★ 1.8k • written 4 months ago by
jochen
• 0
1
vote
2
replies
306
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
8 months ago • updated 6 months ago
A
▴ 40
3
votes
3
replies
323
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2
DEXseq
updated 7 months ago by
Michael Love
37k • written 7 months ago by
k.vitting.seerup
▴ 120
0
votes
1
reply
280
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 6 months ago by
Alejandro Reyes
★ 1.8k • written 10 months ago by
Hahsooni
• 0
0
votes
1
reply
317
views
DTU using DEXSeq (time series data with condition factor)
DTU
DEXSeq
RNADTU
updated 6 months ago by
Alejandro Reyes
★ 1.8k • written 11 months ago by
Nirad
• 0
2
votes
7
replies
445
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
11 months ago
rbenel
▴ 20
0
votes
5
replies
351
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
12 months ago
bioinformatic_trainee
• 0
0
votes
0
replies
246
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures
DEXSeq
12 months ago
Matthias Munz
▴ 10
0
votes
0
replies
233
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
13 months ago
n.tear
▴ 20
0
votes
0
replies
214
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
13 months ago
Matthias Munz
▴ 10
1
vote
6
replies
689
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
updated 14 months ago by
k.vitting.seerup
▴ 120 • written 16 months ago by
jbono
▴ 10
4
votes
5
replies
680
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
15 months ago
Matthias Munz
▴ 10
0
votes
0
replies
295
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
16 months ago
jbono
▴ 10
0
votes
2
replies
385
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
17 months ago
Gaia
• 0
3
votes
2
replies
469
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
17 months ago
Angel
▴ 10
2
votes
2
replies
517
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq
JunctionSeq
RNAseq
QoRTs
18 months ago • updated 17 months ago
n.tear
▴ 20
1
vote
1
reply
430
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 19 months ago by
Alejandro Reyes
★ 1.8k • written 19 months ago by
Anubhav
• 0
0
votes
2
replies
521
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
2.1 years ago • updated 21 months ago
aleksandar.baburski.g
• 0
1
vote
6
replies
2.8k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 21 months ago by
rohitsatyam102
▴ 20 • written 7.4 years ago by
ywu
• 0
0
votes
2
replies
824
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq
estimatedispersions
updated 21 months ago by
rohitsatyam102
▴ 20 • written 4.6 years ago by
brand
• 0
6
votes
7
replies
826
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq
DESeq2
updated 20 months ago by
Michael Love
37k • written 21 months ago by
rohitsatyam102
▴ 20
0
votes
2
replies
343
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 2.1 years ago by
Simon Anders
★ 3.7k • written 2.1 years ago by
lu.la
• 0
0
votes
4
replies
610
views
Calculating per-exon PSI from DEXSeq
DEXSeq
2.1 years ago
Angel Liang
• 0
1
vote
2
replies
447
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 2.1 years ago by
Alejandro Reyes
★ 1.8k • written 2.1 years ago by
Angel Liang
• 0
0
votes
1
reply
298
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu
RNASeq
DEXSeq
DESeq2
updated 2.1 years ago by
Michael Love
37k • written 2.1 years ago by
debatosh das
▴ 10
1
vote
2
replies
501
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq
estimateDispersions
2.2 years ago
aleksandar.baburski.g
• 0
0
votes
2
replies
406
views
DEXSeq HTML report Error
DEXSeq
updated 2.2 years ago by
Kevin Blighe
3.6k • written 2.2 years ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
251
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
2.3 years ago
alexis.weinreb
• 0
1
vote
2
replies
616
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq
python
gtf
gff3
annotation
2.3 years ago
Raito92
▴ 60
0
votes
1
reply
404
views
DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error
DEXSeq
2.3 years ago
knuppdav
• 0
1
vote
3
replies
569
views
DEXSeq with large(ish) number of samples
DEXSeq
exon
memory
dispersions
estimateDispersions
2.3 years ago
andreismolnikov00
• 0
0
votes
0
replies
693
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments
summerizeOverlaps-Method
DEXSeq
updated 2.3 years ago by
Martin Morgan
25k • written 2.3 years ago by
mar.pieraccioli
▴ 10
3
votes
3
replies
695
views
Calculation of Log2 fold change in DEXSeq
DEXSeq
log2foldchange
Tutorial
updated 11 months ago by
rohitsatyam102
▴ 20 • written 2.4 years ago by
tmvarsha
▴ 20
1
vote
2
replies
303
views
How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 2.4 years ago by
Alejandro Reyes
★ 1.8k • written 2.4 years ago by
zliu
• 0
0
votes
3
replies
551
views
DEXSeq Splicing Result with incomplete lines between exons
DEXSeq
Splicing
Exon Usage
2.5 years ago
gunjan.dikshit
• 0
2
votes
6
replies
1.2k
views
featureCount error - cannot identify gene_id
dexseq
rsubread
featureCount
software error
updated 2.7 years ago by
Yang Liao
▴ 340 • written 2.7 years ago by
seung.ho.steven.choi
• 0
0
votes
1
reply
381
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq
splicing
RNAseq
DEXSeq
2.7 years ago
stuart
▴ 10
0
votes
1
reply
308
views
error in DEXSeq estimateExonFoldChanges
dexseq
2.7 years ago
brown.annaleigh
• 0
0
votes
2
replies
416
views
A question about DEXSeq of estimateDispersions
dexseq
updated 2.9 years ago by
glmazzo
• 0 • written 3.0 years ago by
liushang
• 0
0
votes
2
replies
501
views
Issue/Error with DEXSeq design formulae in testForDEU function
deseq2
DEXSeq
BioCParallel
updated 3.0 years ago by
Alejandro Reyes
★ 1.8k • written 3.0 years ago by
acciardo
• 0
1
vote
2
replies
1.2k
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 19 hours ago by
ta_awwad
▴ 10 • written 3.1 years ago by
bruce.hayward
▴ 10
0
votes
2
replies
569
views
DEXSeq error in dexseq_count.py. ValueError: need more than 4 values to unpack
DEXSeq
updated 3.1 years ago by
Simon Anders
★ 3.7k • written 3.1 years ago by
Paola Cornejo
• 0
2
votes
1
reply
446
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq
RNA-Seq
updated 3.2 years ago by
Alejandro Reyes
★ 1.8k • written 3.2 years ago by
justinkablan225
• 0
50 results • Page
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