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
3
replies
124
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
16 days ago • updated 15 days ago
phoebe1354
• 0
0
votes
5
replies
963
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 3.1 years ago by
maslane
• 0
3
votes
9
replies
288
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 weeks ago • updated 28 days ago
Matthew Thornton
▴ 350
3
votes
2
replies
126
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
6 weeks ago • updated 16 days ago
Dakarai
▴ 10
0
votes
1
reply
112
views
Increased number of exons in DEXSeq
DEXSeq
exon
updated 8 weeks ago by
Alejandro Reyes
★ 1.8k • written 8 weeks ago by
jochen
• 0
1
vote
2
replies
245
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
5 months ago • updated 3 months ago
A
▴ 40
3
votes
3
replies
253
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2
DEXseq
updated 4 months ago by
Michael Love
36k • written 4 months ago by
k.vitting.seerup
▴ 100
0
votes
1
reply
222
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 3 months ago by
Alejandro Reyes
★ 1.8k • written 7 months ago by
Hahsooni
• 0
0
votes
1
reply
220
views
DTU using DEXSeq (time series data with condition factor)
DTU
DEXSeq
RNADTU
updated 3 months ago by
Alejandro Reyes
★ 1.8k • written 8 months ago by
Nirad
• 0
2
votes
7
replies
377
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
9 months ago • updated 8 months ago
rbenel
▴ 20
0
votes
5
replies
278
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
9 months ago
bioinformatic_trainee
• 0
0
votes
0
replies
198
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures
DEXSeq
9 months ago
Matthias Munz
▴ 10
0
votes
0
replies
188
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
10 months ago
n.tear
▴ 20
0
votes
0
replies
165
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
10 months ago
Matthias Munz
▴ 10
1
vote
6
replies
608
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
updated 11 months ago by
k.vitting.seerup
▴ 100 • written 13 months ago by
jbono
▴ 10
4
votes
5
replies
591
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
12 months ago
Matthias Munz
▴ 10
0
votes
0
replies
256
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
13 months ago
jbono
▴ 10
0
votes
2
replies
330
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
14 months ago
Gaia
• 0
3
votes
2
replies
413
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
14 months ago
Angel
▴ 10
2
votes
2
replies
448
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq
JunctionSeq
RNAseq
QoRTs
15 months ago • updated 14 months ago
n.tear
▴ 20
1
vote
1
reply
379
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 16 months ago by
Alejandro Reyes
★ 1.8k • written 16 months ago by
Anubhav
• 0
0
votes
2
replies
455
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
23 months ago • updated 18 months ago
aleksandar.baburski.g
• 0
1
vote
6
replies
2.8k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 18 months ago by
rohitsatyam102
▴ 20 • written 7.2 years ago by
ywu
• 0
0
votes
2
replies
765
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq
estimatedispersions
updated 18 months ago by
rohitsatyam102
▴ 20 • written 4.4 years ago by
brand
• 0
6
votes
7
replies
748
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq
DESeq2
updated 17 months ago by
Michael Love
36k • written 18 months ago by
rohitsatyam102
▴ 20
0
votes
2
replies
303
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 22 months ago by
Simon Anders
★ 3.7k • written 22 months ago by
lu.la
• 0
0
votes
4
replies
522
views
Calculating per-exon PSI from DEXSeq
DEXSeq
22 months ago
Angel Liang
• 0
1
vote
2
replies
372
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 22 months ago by
Alejandro Reyes
★ 1.8k • written 22 months ago by
Angel Liang
• 0
0
votes
1
reply
259
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu
RNASeq
DEXSeq
DESeq2
updated 22 months ago by
Michael Love
36k • written 22 months ago by
debatosh das
▴ 10
1
vote
2
replies
443
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq
estimateDispersions
23 months ago
aleksandar.baburski.g
• 0
0
votes
2
replies
350
views
DEXSeq HTML report Error
DEXSeq
updated 23 months ago by
Kevin Blighe
3.5k • written 23 months ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
207
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
2.0 years ago
alexis.weinreb
• 0
1
vote
2
replies
481
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq
python
gtf
gff3
annotation
2.0 years ago
Raito92
▴ 60
0
votes
1
reply
339
views
DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error
DEXSeq
2.1 years ago
knuppdav
• 0
1
vote
3
replies
469
views
DEXSeq with large(ish) number of samples
DEXSeq
exon
memory
dispersions
estimateDispersions
2.1 years ago
andreismolnikov00
• 0
0
votes
0
replies
569
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments
summerizeOverlaps-Method
DEXSeq
updated 2.1 years ago by
Martin Morgan
25k • written 2.1 years ago by
mar.pieraccioli
▴ 10
3
votes
3
replies
545
views
Calculation of Log2 fold change in DEXSeq
DEXSeq
log2foldchange
Tutorial
updated 8 months ago by
rohitsatyam102
▴ 20 • written 2.1 years ago by
tmvarsha
▴ 20
1
vote
2
replies
272
views
How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 2.1 years ago by
Alejandro Reyes
★ 1.8k • written 2.1 years ago by
zliu
• 0
0
votes
3
replies
499
views
DEXSeq Splicing Result with incomplete lines between exons
DEXSeq
Splicing
Exon Usage
2.3 years ago
gunjan.dikshit
• 0
2
votes
6
replies
963
views
featureCount error - cannot identify gene_id
dexseq
rsubread
featureCount
software error
updated 2.5 years ago by
Yang Liao
▴ 340 • written 2.5 years ago by
seung.ho.steven.choi
• 0
0
votes
1
reply
330
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq
splicing
RNAseq
DEXSeq
2.5 years ago
stuart
▴ 10
0
votes
1
reply
282
views
error in DEXSeq estimateExonFoldChanges
dexseq
2.5 years ago
brown.annaleigh
• 0
0
votes
2
replies
385
views
A question about DEXSeq of estimateDispersions
dexseq
updated 2.6 years ago by
glmazzo
• 0 • written 2.7 years ago by
liushang
• 0
0
votes
2
replies
466
views
Issue/Error with DEXSeq design formulae in testForDEU function
deseq2
DEXSeq
BioCParallel
updated 2.7 years ago by
Alejandro Reyes
★ 1.8k • written 2.7 years ago by
acciardo
• 0
0
votes
1
reply
1.1k
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 2.8 years ago by
James W. MacDonald
59k • written 2.8 years ago by
bruce.hayward
• 0
0
votes
2
replies
535
views
DEXSeq error in dexseq_count.py. ValueError: need more than 4 values to unpack
DEXSeq
updated 2.9 years ago by
Simon Anders
★ 3.7k • written 2.9 years ago by
Paola Cornejo
• 0
2
votes
1
reply
404
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq
RNA-Seq
updated 3.0 years ago by
Alejandro Reyes
★ 1.8k • written 3.0 years ago by
justinkablan225
• 0
2
votes
3
replies
468
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 3.0 years ago by
Hervé Pagès
15k • written 3.0 years ago by
story.benjamin
▴ 10
0
votes
6
replies
720
views
DEXSeq dispersion outlier
DEXSeq
dispersion
pvalue
3.0 years ago
fiona.dick91
▴ 10
1
vote
3
replies
583
views
null model and DEXSeqDataSet object in DEXSEQ
deseq2
dexseq
3.0 years ago
gv
▴ 40
50 results • Page
1 of 1
Recent ...
Replies
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
James W. MacDonald
59k
We have progressed past the point where I show you how to do things using Bioconductor packages, and into the realm where I start telling y…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
Yang Shi
• 0
Thanks sir! As your mentioned here, 12-15 means cutoff value about 4? Could I select the reflection point as the "point" that starts to ha…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
James W. MacDonald
59k
It's a non-scientific selection. The Nonspecific probes are meant to be sequences that are not found in nature, so any binding is due to cr…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
Yang Shi
• 0
Thanks for your excellent reply sir! But there are still some points confused me. (1).dbGetQuery get 93 kinds of probes. Would be okay for …
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
by
Kevin Blighe
3.5k
Great! problem solved, then?
Votes
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Comment: Quantile Normalization after rma or not?
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
Comment: How to best visualize multi-level transcriptomics experiment data?
Awards
• All
Scholar
to
James W. MacDonald
59k
Popular Question
to
Rory Stark
★ 4.4k
Popular Question
to
Gyan Prakash Mishra
• 0
Scholar
to
ATpoint
★ 1.2k
Teacher
to
Gordon Smyth
45k
Locations
• All
Miami Shores, FL,
3 minutes ago
Portugal,
11 minutes ago
United States,
11 minutes ago
Switzerland,
15 minutes ago
United States,
18 minutes ago
Traffic: 828 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