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Showing :
dexseq
•
reset
0
votes
4
replies
98
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
5 days ago • updated 18 hours ago
jbono
• 0
0
votes
0
replies
52
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
9 days ago
jbono
• 0
0
votes
2
replies
93
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
27 days ago • updated 23 days ago
Gaia
• 0
3
votes
2
replies
120
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
5 weeks ago
Angel
▴ 10
2
votes
2
replies
105
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq
JunctionSeq
RNAseq
QoRTs
8 weeks ago • updated 5 weeks ago
n.tear
▴ 10
1
vote
1
reply
95
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3 months ago by
Alejandro Reyes
★ 1.7k • written 3 months ago by
Anubhav
• 0
0
votes
2
replies
172
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
9 months ago • updated 4 months ago
aleksandar.baburski.g
• 0
1
vote
6
replies
2.3k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 5 months ago by
rohitsatyam102
▴ 10 • written 6.1 years ago by
ywu
• 0
0
votes
2
replies
487
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq
estimatedispersions
updated 5 months ago by
rohitsatyam102
▴ 10 • written 3.3 years ago by
brand
• 0
5
votes
7
replies
344
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq
DESeq2
updated 3 months ago by
Michael Love
32k • written 5 months ago by
rohitsatyam102
▴ 10
0
votes
4
replies
519
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
updated 5 months ago by
Qub
• 0 • written 2.0 years ago by
maslane
• 0
0
votes
2
replies
114
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 8 months ago by
Simon Anders
★ 3.6k • written 9 months ago by
lu.la
• 0
0
votes
4
replies
127
views
Calculating per-exon PSI from DEXSeq
DEXSeq
8 months ago
Angel Liang
• 0
1
vote
2
replies
107
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 9 months ago by
Alejandro Reyes
★ 1.7k • written 9 months ago by
Angel Liang
• 0
0
votes
1
reply
83
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu
RNASeq
DEXSeq
DESeq2
updated 9 months ago by
Michael Love
32k • written 9 months ago by
debatosh das
▴ 10
1
vote
2
replies
130
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq
estimateDispersions
10 months ago
aleksandar.baburski.g
• 0
0
votes
2
replies
117
views
DEXSeq HTML report Error
DEXSeq
updated 10 months ago by
Kevin Blighe
2.7k • written 10 months ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
63
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
11 months ago
alexis.weinreb
• 0
1
vote
2
replies
142
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq
python
gtf
gff3
annotation
11 months ago
Raito92
▴ 40
0
votes
1
reply
100
views
DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error
DEXSeq
11 months ago
knuppdav
• 0
1
vote
3
replies
150
views
DEXSeq with large(ish) number of samples
DEXSeq
exon
memory
dispersions
estimateDispersions
11 months ago
andreismolnikov00
• 0
0
votes
0
replies
121
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments
summerizeOverlaps-Method
DEXSeq
updated 12 months ago by
Martin Morgan
25k • written 12 months ago by
mar.pieraccioli
▴ 10
0
votes
2
replies
98
views
Calculation of Log2 fold change in DEXSeq
DEXSeq
log2foldchange
Tutorial
updated 12 months ago by
Martin Morgan
25k • written 12 months ago by
tmvarsha
• 0
1
vote
2
replies
98
views
How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 12 months ago by
Alejandro Reyes
★ 1.7k • written 12 months ago by
zliu
• 0
0
votes
3
replies
215
views
DEXSeq Splicing Result with incomplete lines between exons
DEXSeq
Splicing
Exon Usage
14 months ago
gunjan.dikshit
• 0
2
votes
6
replies
279
views
featureCount error - cannot identify gene_id
dexseq
rsubread
featureCount
software error
updated 16 months ago by
Yang Liao
▴ 220 • written 16 months ago by
seung.ho.steven.choi
• 0
0
votes
1
reply
135
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq
splicing
RNAseq
DEXSeq
16 months ago
stuart
▴ 10
0
votes
1
reply
125
views
error in DEXSeq estimateExonFoldChanges
dexseq
16 months ago
brown.annaleigh
• 0
0
votes
2
replies
205
views
A question about DEXSeq of estimateDispersions
dexseq
updated 18 months ago by
glmazzo
• 0 • written 20 months ago by
liushang
• 0
0
votes
2
replies
237
views
Issue/Error with DEXSeq design formulae in testForDEU function
deseq2
DEXSeq
BioCParallel
updated 19 months ago by
Alejandro Reyes
★ 1.7k • written 19 months ago by
acciardo
• 0
0
votes
1
reply
559
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 21 months ago by
James W. MacDonald
56k • written 21 months ago by
bruce.hayward
• 0
0
votes
2
replies
247
views
DEXSeq error in dexseq_count.py. ValueError: need more than 4 values to unpack
DEXSeq
updated 21 months ago by
Simon Anders
★ 3.6k • written 22 months ago by
Paola Cornejo
• 0
2
votes
1
reply
234
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq
RNA-Seq
updated 22 months ago by
Alejandro Reyes
★ 1.7k • written 22 months ago by
justinkablan225
• 0
2
votes
3
replies
238
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 23 months ago by
Hervé Pagès
14k • written 23 months ago by
story.benjamin
▴ 10
0
votes
6
replies
395
views
DEXSeq dispersion outlier
DEXSeq
dispersion
pvalue
23 months ago
fiona.dick91
▴ 10
1
vote
3
replies
249
views
null model and DEXSeqDataSet object in DEXSEQ
deseq2
dexseq
23 months ago
gv
▴ 40
2
votes
6
replies
317
views
estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2
dexseq
23 months ago
gv
▴ 40
1
vote
6
replies
355
views
How to install DEXSeq on R 3.4.4
DEXSEq
Linux
updated 23 months ago by
Alejandro Reyes
★ 1.7k • written 23 months ago by
justinkablan225
• 0
1
vote
1
reply
474
views
rnaseqDTU log2fold change DEXSeq
DEXSeq
DTU
salmon
rnaseqDTU
foldchange
updated 23 months ago by
Michael Love
32k • written 2.2 years ago by
fiona.dick91
▴ 10
0
votes
11
replies
365
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU
DRIMseq
DEXseq
rna-seq
2.0 years ago
saddamhusain77
• 0
0
votes
2
replies
232
views
DEXSeq With Reduced Annotations
dexseq
reduced annotation set
2.1 years ago
sumeet460
• 0
1
vote
2
replies
393
views
Normalized transcript/exon counts for network analysis
drimseq
dexseq
wgcna
sva
updated 2.1 years ago by
Gosia Nowicka
▴ 80 • written 2.2 years ago by
maya.kappil
▴ 10
2
votes
4
replies
397
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
2.2 years ago
d-joester
▴ 20
0
votes
4
replies
395
views
tximport: Error in medianLengthOverIsoform
tximport
deseq2
dexseq
2.2 years ago
d-joester
▴ 20
0
votes
1
reply
283
views
DEXSeq: controlling for cell composition
dexseq
updated 2.2 years ago by
Alejandro Reyes
★ 1.7k • written 2.3 years ago by
skinnider
• 0
0
votes
1
reply
309
views
Can DEXseq be used for splicing QTL analysis?
dexseq
splicing
sqtl
qtl
updated 2.2 years ago by
Alejandro Reyes
★ 1.7k • written 2.2 years ago by
rtunney2
• 0
0
votes
3
replies
378
views
How to get missing columns in DEXSeq analysis (exon usage coefficients)
dexseq
dexseqalt
2.2 years ago
mjrarcher
• 0
0
votes
1
reply
380
views
Add interaction term between variables to DEXSeq design
DEXSeq
interaction
2.3 years ago
zhenzuo2
• 0
0
votes
0
replies
249
views
DEXSeq: How to reduce compute time for estimating dispersions for large datasets.
dexseq
estimatedispersions
large dataset
2.3 years ago
mjrarcher
• 0
0
votes
5
replies
409
views
DEXSeq 1.26.0 running very slowly (stuck?)
dexseq
2.3 years ago
Lance Parsons
• 0
321 results • Page
1 of 7
Recent ...
Replies
Answer: DepMap copy number
by
Laurent Gatto
1.5k
Hi Danny - sorry for the delay in answering, I hadn't set `depmap` as a tag yet. Yes, that bug has been fixed in the devel version.
Answer: High fold change reported for comparison of samples with zero values in all samp
by
James W. MacDonald
56k
The universal recommendation is to remove all genes with consistently low (or all zero) expression values prior to doing any modeling. It i…
Comment: Sample quality weights for RNA-seq
by
Naomi Altman
★ 6.0k
Thanks Michael. I'll try that. (Limma folks, I'd still love to hear from you.)
Answer: Installation error if message implemented in .Rprofile
by
Mike Smith
★ 4.9k
A similar issue has been reported recently for rhdf5filters (https://github.com/grimbough/rhdf5filters/issues/11) and rhdf5 (https://github…
Comment: Couldn't load org.Hs.eg.db
by
Xulei Huo
• 0
That does not work, i have tried it.
Votes
Answer: TargetsFile. Where it is?
Answer: TargetsFile. Where it is?
Comment: TargetsFile. Where it is?
Comment: Using DESeq2 to identify changing transcriptional activity in a metagenome
Answer: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
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