Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
DEXSEq
•
reset
0
votes
2
replies
160
views
Swimming downstream: transcript fold changes
DEXSeq
stageR
4 weeks ago
jbono
▴ 10
0
votes
1
reply
159
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
5 weeks ago
NiKo
• 0
0
votes
3
replies
421
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 3 months ago by
Alejandro Reyes
★ 1.9k • written 3 months ago by
Alice
• 0
0
votes
3
replies
500
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 4 months ago by
Hervé Pagès
16k • written 4 months ago by
anavmar1
• 0
0
votes
2
replies
334
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
4 months ago • updated 3 months ago
yr542
• 0
8
votes
7
replies
1.4k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 5 months ago by
alexandresegers
▴ 20 • written 13 months ago by
jeremymsimon
▴ 20
1
vote
5
replies
592
views
DEXSeq output included non-exist exons
DEXSeq
exon_definition
exon
updated 5 months ago by
Alejandro Reyes
★ 1.9k • written 5 months ago by
zhangpeng1202
• 0
0
votes
0
replies
242
views
Recommendation sought for differential exon usage of a single gene
isofor
DEXSeq
DifferentialSplicing
6 months ago
nick_brittain55
• 0
0
votes
0
replies
254
views
Error while performing DEXseq
DEXSeq
6 months ago
vipul14
• 0
0
votes
0
replies
290
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
9 months ago
Ben J
• 0
0
votes
2
replies
612
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
10 months ago
Ben J
• 0
0
votes
0
replies
409
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 12 months ago by
Michael Love
41k • written 12 months ago by
barrypraveen
• 0
0
votes
1
reply
614
views
plotDEXSeq error?
DEXSeq
dex
12 months ago
barrypraveen
• 0
1
vote
4
replies
754
views
DEXseq batch removal
DEXSeq
updated 14 months ago by
Alejandro Reyes
★ 1.9k • written 14 months ago by
ta_awwad
▴ 10
0
votes
0
replies
322
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
15 months ago
Matthias Munz
▴ 10
0
votes
0
replies
379
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
16 months ago
osieman52
• 0
1
vote
2
replies
650
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
16 months ago
Delta._.43
▴ 20
0
votes
1
reply
659
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
18 months ago
NIK
• 0
0
votes
4
replies
1.1k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 18 months ago by
jeroen.gilis
▴ 90 • written 19 months ago by
phoebe1354
• 0
0
votes
5
replies
1.7k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 4.7 years ago by
maslane
• 0
6
votes
11
replies
2.4k
views
DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq)
DEXSeq
updated 8 months ago by
EChambers
• 0 • written 20 months ago by
Matthew Thornton
▴ 350
3
votes
2
replies
752
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
20 months ago • updated 19 months ago
Dakarai
▴ 10
1
vote
1
reply
527
views
Increased number of exons in DEXSeq
DEXSeq
exon
updated 20 months ago by
Alejandro Reyes
★ 1.9k • written 20 months ago by
jochen
• 0
1
vote
2
replies
723
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.0 years ago • updated 22 months ago
A
▴ 40
3
votes
3
replies
893
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2
DEXseq
updated 23 months ago by
Michael Love
41k • written 23 months ago by
k.vitting.seerup
▴ 120
0
votes
1
reply
711
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 22 months ago by
Alejandro Reyes
★ 1.9k • written 2.2 years ago by
Hahsooni
• 0
1
vote
1
reply
912
views
DTU using DEXSeq (time series data with condition factor)
DTU
DEXSeq
RNADTU
updated 22 months ago by
Alejandro Reyes
★ 1.9k • written 2.3 years ago by
Nirad
▴ 10
2
votes
7
replies
1.1k
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
2.3 years ago
rbenel
▴ 30
0
votes
5
replies
1.0k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
2.3 years ago
bioinformatic_trainee
▴ 10
0
votes
0
replies
671
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures
DEXSeq
2.4 years ago
Matthias Munz
▴ 10
0
votes
0
replies
522
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
2.4 years ago
n.tear
▴ 20
0
votes
0
replies
532
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.5 years ago
Matthias Munz
▴ 10
1
vote
6
replies
1.3k
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
updated 2.5 years ago by
k.vitting.seerup
▴ 120 • written 2.7 years ago by
jbono
▴ 10
4
votes
5
replies
1.6k
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
2.6 years ago
Matthias Munz
▴ 10
0
votes
0
replies
712
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
2.7 years ago
jbono
▴ 10
0
votes
2
replies
844
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
2.7 years ago
Gaia
• 0
3
votes
2
replies
863
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
2.8 years ago • updated 2.7 years ago
Angel
▴ 10
2
votes
2
replies
1.0k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq
JunctionSeq
RNAseq
QoRTs
2.8 years ago • updated 2.7 years ago
n.tear
▴ 20
1
vote
1
reply
827
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 2.9 years ago by
Alejandro Reyes
★ 1.9k • written 2.9 years ago by
Anubhav
• 0
0
votes
2
replies
1.0k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
3.5 years ago • updated 3.1 years ago
aleksandar.baburski.g
• 0
1
vote
6
replies
3.7k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.1 years ago by
rohitsatyam102
▴ 20 • written 8.7 years ago by
ywu
• 0
0
votes
2
replies
1.3k
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq
estimatedispersions
updated 3.1 years ago by
rohitsatyam102
▴ 20 • written 5.9 years ago by
brand
• 0
6
votes
7
replies
1.5k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq
DESeq2
updated 3.0 years ago by
Michael Love
41k • written 3.1 years ago by
rohitsatyam102
▴ 20
0
votes
2
replies
721
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 3.4 years ago by
Simon Anders
★ 3.7k • written 3.4 years ago by
lu.la
• 0
0
votes
4
replies
1.3k
views
Calculating per-exon PSI from DEXSeq
DEXSeq
3.4 years ago
Angel Liang
• 0
1
vote
2
replies
989
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 3.4 years ago by
Alejandro Reyes
★ 1.9k • written 3.4 years ago by
Angel Liang
• 0
0
votes
1
reply
611
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu
RNASeq
DEXSeq
DESeq2
updated 3.4 years ago by
Michael Love
41k • written 3.4 years ago by
debatosh das
▴ 10
1
vote
2
replies
976
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq
estimateDispersions
3.5 years ago
aleksandar.baburski.g
• 0
0
votes
2
replies
751
views
DEXSeq HTML report Error
DEXSeq
updated 3.5 years ago by
Kevin Blighe
3.9k • written 3.5 years ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
565
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
3.6 years ago
alexis.weinreb
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Correct the batch effect in methylation analysis in R
by
kyj2226
• 0
Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…
Answer: Correct the batch effect in methylation analysis in R
by
Gordon Smyth
49k
You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model. …
Answer: Agilent Microarray Gene Oncology analysis gone wrong
by
Gordon Smyth
49k
Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…
Comment: Normalised counts from RUVg in RUVSeq
by
Shaimaa Gamal
• 0
Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
Comment: enrichGOgradient color change
by
James W. MacDonald
64k
You could look at my answer and extrapolate from there.
Votes
Answer: Correct the batch effect in methylation analysis in R
Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
Awards
• All
Popular Question
to
Gordon Smyth
49k
Popular Question
to
Lluís Revilla Sancho
▴ 720
Popular Question
to
Frederik Ziebell
▴ 20
Popular Question
to
Sam
▴ 10
Scholar
to
Rory Stark
★ 5.1k
Locations
• All
WEHI, Melbourne, Australia,
21 minutes ago
South Korea,
33 minutes ago
Russia,
41 minutes ago
Russia,
59 minutes ago
The city by the bay,
2 hours ago
Traffic: 588 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6