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
1
vote
10
replies
384
views
Obtaining pheno data from CEL files
GEO
affy
17 days ago • updated 10 days ago
Kurtis
• 0
0
votes
1
reply
486
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 10 days ago by
ivorychan7777
• 0 • written 14 months ago by
609b0d25
• 0
2
votes
6
replies
310
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
11 days ago
Chris
• 0
0
votes
1
reply
147
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 11 days ago by
James W. MacDonald
65k • written 12 days ago by
BCS12
• 0
0
votes
0
replies
104
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
11 days ago
arne.sahm
• 0
0
votes
0
replies
73
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
11 days ago
Wolfgang Huber
★ 13k
0
votes
4
replies
281
views
Help with design.matrix
limma
14 days ago • updated 13 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
139
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
avery
• 0
1
vote
3
replies
221
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
108
views
Granges regionCounts not returning the expected number of entries
methylKit
15 days ago • updated 14 days ago
Modoc Kesner
▴ 10
1
vote
2
replies
191
views
MethylKit read issue
methylKit
updated 14 days ago by
James W. MacDonald
65k • written 19 days ago by
CHEN
• 0
1
vote
2
replies
3.0k
views
Extract genes from ggvenn?
ggvenn
updated 14 days ago by
Michael
▴ 10 • written 23 months ago by
axe880
• 0
0
votes
1
reply
528
views
CopywriteR output
CopywriteR
updated 14 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 0
0
votes
2
replies
261
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
19 days ago • updated 14 days ago
fer_talavera
• 0
0
votes
0
replies
122
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
14 days ago
andromeda
• 0
0
votes
2
replies
133
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
joshua.mannheimer
• 0
2
votes
2
replies
158
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 14 days ago by
ATpoint
★ 4.0k • written 14 days ago by
Dario Strbenac
★ 1.5k
2
votes
5
replies
996
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 14 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
1
vote
4
replies
398
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 15 days ago by
Gordon Smyth
50k • written 16 days ago by
jari.karppinen
• 0
5
votes
25
replies
790
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 15 days ago by
Gordon Smyth
50k • written 25 days ago by
Jitendra
▴ 10
0
votes
0
replies
77
views
flowDensity on a flowset
flowDensity
15 days ago
fredrikwallberg
• 0
0
votes
2
replies
157
views
Gene Ontology doubt
microbiomeExplorer
19 days ago • updated 15 days ago
Bhawna
• 0
1
vote
1
reply
149
views
DESeq2 - Missing values in count matrix
DESeq2
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
Hong Thu
• 0
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 15 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
1
reply
191
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 15 days ago by
Tim Peters
▴ 170 • written 16 days ago by
Kim
• 0
0
votes
0
replies
70
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
16 days ago
Macsue
• 0
1
vote
6
replies
393
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 16 days ago by
Michael Love
41k • written 16 days ago by
RL
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 16 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
2
replies
730
views
error in install immunedeconv
Install
updated 16 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
0
votes
2
replies
162
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
16 days ago
Gimena
• 0
0
votes
2
replies
139
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
16 days ago
Marianna
▴ 20
0
votes
2
replies
143
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
17 days ago • updated 16 days ago
michelafrancesconi8
• 0
1
vote
1
reply
130
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
17 days ago • updated 16 days ago
Layal
• 0
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 17 days ago by
Tim Peters
▴ 170 • written 4 months ago by
rae.alshammari
▴ 10
0
votes
2
replies
308
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
28 days ago • updated 17 days ago
Gordon
• 0
0
votes
4
replies
217
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 17 days ago by
Michael Love
41k • written 18 days ago by
Aidan
• 0
0
votes
2
replies
205
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
22 days ago • updated 17 days ago
w.cookson
• 0
0
votes
4
replies
386
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
18 days ago • updated 17 days ago
Lucy
▴ 60
0
votes
1
reply
128
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 17 days ago by
James W. MacDonald
65k • written 19 days ago by
ja569116
• 0
0
votes
1
reply
112
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
Reeya
• 0
0
votes
7
replies
322
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
20 days ago • updated 17 days ago
needNGS
• 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 17 days ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
0
votes
2
replies
156
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
18 days ago • updated 17 days ago
Seongsu
• 0
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 17 days ago by
Gordon Smyth
50k • written 11.5 years ago by
Maria Keays
▴ 30
0
votes
1
reply
91
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
Leyre
• 0
0
votes
1
reply
148
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 18 days ago by
Michael Love
41k • written 21 days ago by
saadmurtazakhan
▴ 10
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 19 days ago by
Wolfgang Huber
★ 13k • written 9 months ago by
Jane
▴ 10
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 19 days ago by
isaac.vock
• 0 • written 7.8 years ago by
Jon Manning
▴ 90
0
votes
3
replies
307
views
Statistical test
NewWave
written 4 months ago by
mario
• 0
3
votes
5
replies
327
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 20 days ago by
Gordon Smyth
50k • written 22 days ago by
Fabian
• 0
45,551 results • Page
3 of 912
Recent ...
Replies
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Awards
• All
Popular Question
to
James W. MacDonald
65k
Popular Question
to
shepherl
3.8k
Popular Question
to
BioinfGuru
▴ 30
Popular Question
to
Gordon Smyth
50k
Scholar
to
Peter Hickey
▴ 740
Locations
• All
United States,
24 minutes ago
France,
29 minutes ago
WEHI, Melbourne, Australia,
36 minutes ago
Vietnam,
49 minutes ago
United States,
1 hour ago
Traffic: 499 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