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 :
Biseq
•
reset
0
votes
1
reply
1.0k
views
Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
3.7 years ago
thomas.koefoed
• 0
0
votes
0
replies
1.1k
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
5.3 years ago
i.s.castanho
• 0
0
votes
1
reply
1.4k
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph
.cov
wig
biseq
coverage
5.3 years ago
akhaira
• 0
0
votes
1
reply
1.1k
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
5.3 years ago
akhaira
• 0
2
votes
8
replies
1.6k
views
Reason for NA in table after beta regression?
biseq
beta regression
5.3 years ago
akhaira
• 0
0
votes
0
replies
722
views
What values to include for predictedMethNull in BiSeq
Biseq
5.3 years ago
akhaira
• 0
2
votes
10
replies
2.1k
views
How do you use the readBismark command in BiSeq properly?
BiSeq
DMR
updated 5.4 years ago by
James W. MacDonald
68k • written 5.4 years ago by
akhaira
• 0
1
vote
0
replies
908
views
Understanding ColData in BiSeq
BiSeq
Coldata
5.4 years ago
akhaira
• 0
0
votes
1
reply
995
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
5.5 years ago
AishaD
• 0
0
votes
1
reply
957
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
5.6 years ago
i.s.castanho
• 0
0
votes
0
replies
1.1k
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq
Wald test
Beta regression
6.7 years ago
mira
• 0
0
votes
1
reply
1.3k
views
Biseq installation error
biseq
package installation
r
updated 6.8 years ago by
Martin Morgan
25k • written 6.8 years ago by
lwh863
• 0
0
votes
0
replies
1.2k
views
BiSeq: Read in Relative Methylation data from CCLE
biseq
ccle
7.2 years ago
spr
▴ 10
0
votes
1
reply
1.4k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 7.8 years ago by
Gordon Smyth
53k • written 7.8 years ago by
ahmad.moousavi
• 0
0
votes
1
reply
1.5k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
8.6 years ago
l.eijssen
• 0
0
votes
3
replies
1.7k
views
BiSeq. Model beta regression on resampled data.
biseq
methylation
dmr analysis
updated 8.8 years ago by
Katja Hebestreit
▴ 130 • written 8.8 years ago by
jjalmagro
• 0
0
votes
6
replies
2.4k
views
BiSeq trimClusters error
biseq
error
trimClusters
updated 9.7 years ago by
Katja Hebestreit
▴ 130 • written 9.8 years ago by
kms68
• 0
1
vote
0
replies
2.0k
views
Multiple linear regression model for DMR detection?
methylation
linear model
dmr
bsseq
biseq
9.9 years ago
enricoferrero
▴ 680
4
votes
4
replies
2.3k
views
Unable to read data using readBismark in BiSeq
BiSeq
readBismark
updated 10.0 years ago by
James W. MacDonald
68k • written 10.0 years ago by
Neel Aluru
▴ 460
1
vote
2
replies
3.1k
views
BS-seq differential methylation analysis using continuous variable
dmr
methylation
deseq2
bsseq
biseq
updated 10.0 years ago by
Kasper Daniel Hansen
★ 6.5k • written 10.0 years ago by
enricoferrero
▴ 680
2
votes
15
replies
4.3k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
10.5 years ago • updated 10.4 years ago
mnaymik
▴ 10
0
votes
5
replies
2.6k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
10.5 years ago
maria.maqueda
• 0
0
votes
3
replies
2.1k
views
BiSeq - readBismark error
BiSeq
BiSeq
updated 11.7 years ago by
David Iles
▴ 130 • written 11.7 years ago by
Hans-Ulrich Klein
▴ 330
23 results • Page
1 of 1
Recent ...
Replies
Answer: Using DESeq2 for age prediction
by
ATpoint
★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
Awards
• All
Popular Question
to
Gordon Smyth
53k
Popular Question
to
Matej
• 0
Popular Question
to
Hervé Pagès
16k
Popular Question
to
Josef Frank
• 0
Popular Question
to
dan.gatti
• 0
Locations
• All
United States,
35 minutes ago
The city by the bay,
55 minutes ago
United States,
1 hour ago
United States,
2 hours ago
United States,
3 hours ago
Traffic: 1333 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