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
3
votes
6
replies
264
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
21 days ago • updated 20 days ago
nhaus
▴ 30
0
votes
0
replies
97
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
21 days ago
communication
• 0
0
votes
6
replies
323
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 21 days ago by
Tim Peters
▴ 170 • written 29 days ago by
s.malik
• 0
0
votes
0
replies
126
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
21 days ago
Eryn
• 0
0
votes
0
replies
84
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
21 days ago
Dennis
• 0
1
vote
6
replies
479
views
GSVA on separate healthy and disease datasets
GSVA
updated 22 days ago by
James W. MacDonald
65k • written 23 days ago by
Lucy
▴ 60
0
votes
1
reply
333
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 22 days ago by
Lluís Revilla Sancho
▴ 730 • written 7 months ago by
karmasstark
• 0
0
votes
1
reply
133
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 22 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Merav
• 0
0
votes
0
replies
105
views
ggtree tip label position (depth)
ggtree
23 days ago • updated 22 days ago
Roope
• 0
0
votes
2
replies
214
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 22 days ago by
Michael Love
41k • written 27 days ago by
nhaus
▴ 30
0
votes
1
reply
157
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 22 days ago by
Michael Love
41k • written 22 days ago by
Adelaide
• 0
0
votes
2
replies
233
views
Regressing out batch effects
DESeq2
updated 22 days ago by
Michael Love
41k • written 27 days ago by
kys91240
• 0
0
votes
1
reply
146
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
zh9118
• 0
1
vote
10
replies
438
views
Obtaining pheno data from CEL files
GEO
affy
29 days ago • updated 23 days ago
Kurtis
• 0
0
votes
1
reply
507
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 23 days ago by
ivorychan7777
• 0 • written 15 months ago by
609b0d25
• 0
2
votes
6
replies
385
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
23 days ago
Chris
• 0
0
votes
1
reply
176
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 23 days ago by
James W. MacDonald
65k • written 24 days ago by
BCS12
• 0
0
votes
0
replies
139
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
24 days ago
arne.sahm
• 0
0
votes
0
replies
94
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
24 days ago
Wolfgang Huber
★ 13k
0
votes
4
replies
302
views
Help with design.matrix
limma
26 days ago • updated 25 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
157
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 26 days ago by
Gordon Smyth
50k • written 26 days ago by
avery
• 0
1
vote
3
replies
240
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
126
views
Granges regionCounts not returning the expected number of entries
methylKit
27 days ago • updated 26 days ago
Modoc Kesner
▴ 10
1
vote
2
replies
224
views
MethylKit read issue
methylKit
updated 26 days ago by
James W. MacDonald
65k • written 4 weeks ago by
CHEN
• 0
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 26 days ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
0
votes
1
reply
551
views
CopywriteR output
CopywriteR
updated 26 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 0
0
votes
2
replies
287
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
4 weeks ago • updated 26 days ago
fer_talavera
• 0
0
votes
0
replies
141
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
26 days ago
andromeda
• 0
0
votes
2
replies
159
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
joshua.mannheimer
• 0
2
votes
2
replies
183
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 27 days ago by
ATpoint
★ 4.1k • written 27 days ago by
Dario Strbenac
★ 1.5k
2
votes
5
replies
1.0k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 27 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
1
vote
4
replies
426
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 27 days ago by
Gordon Smyth
50k • written 29 days ago by
jari.karppinen
• 0
5
votes
25
replies
865
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 27 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
0
votes
0
replies
98
views
flowDensity on a flowset
flowDensity
27 days ago
fredrikwallberg
• 0
0
votes
2
replies
174
views
Gene Ontology doubt
microbiomeExplorer
4 weeks ago • updated 27 days ago
Bhawna
• 0
1
vote
1
reply
160
views
DESeq2 - Missing values in count matrix
DESeq2
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
Hong Thu
• 0
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 28 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
1
reply
232
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 28 days ago by
Tim Peters
▴ 170 • written 28 days ago by
Kim
• 0
0
votes
0
replies
86
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
28 days ago
Macsue
• 0
1
vote
6
replies
419
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 28 days ago by
Michael Love
41k • written 28 days ago by
RL
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 28 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
2
replies
754
views
error in install immunedeconv
Install
updated 28 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
0
votes
2
replies
183
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
29 days ago • updated 28 days ago
Gimena
• 0
0
votes
2
replies
155
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
29 days ago
Marianna
▴ 20
0
votes
2
replies
166
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
4 weeks ago • updated 29 days ago
michelafrancesconi8
• 0
1
vote
1
reply
148
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago • updated 29 days ago
Layal
• 0
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 29 days ago by
Tim Peters
▴ 170 • written 5 months ago by
rae.alshammari
▴ 10
0
votes
2
replies
347
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
5 weeks ago • updated 29 days ago
Gordon
• 0
0
votes
4
replies
251
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Aidan
• 0
0
votes
2
replies
226
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
4 weeks ago • updated 29 days ago
w.cookson
• 0
45,603 results • Page
4 of 913
Recent ...
Replies
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Awards
• All
Popular Question
to
rohitsatyam102
▴ 20
Popular Question
to
shepherl
3.8k
Popular Question
to
siajunren
• 0
Scholar
to
Rory Stark
★ 5.2k
Popular Question
to
tangming2005
▴ 190
Locations
• All
Belgium,
7 minutes ago
France,
15 minutes ago
Germany,
18 minutes ago
India,
21 minutes ago
France,
27 minutes ago
Traffic: 918 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