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 :
RNA
•
reset
0
votes
3
replies
491
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO
rnaseqGene
RNA
3 months ago
gallantk5
• 0
0
votes
5
replies
949
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 8 months ago by
James W. MacDonald
67k • written 8 months ago by
Gordon
• 0
0
votes
1
reply
525
views
Running Deseq2 with all samples vs samples for each comparison separately
RNA
DESeq2
updated 9 months ago by
Michael Love
42k • written 9 months ago by
manuel
• 0
0
votes
2
replies
1.4k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt
ensembldb
RNA
ensembl
updated 19 months ago by
Johannes Rainer
★ 2.1k • written 19 months ago by
Christopher
• 0
3
votes
6
replies
2.5k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2
edgeR
RNA
limma
Normalization
23 months ago
Sara
• 0
0
votes
0
replies
663
views
Correct GFF3 translation for FeatureCounts
RNASeq
FeatureCounts
Rna
2.0 years ago
rridley3
• 0
1
vote
1
reply
900
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 2.1 years ago by
ATpoint
★ 4.5k • written 2.1 years ago by
Mohamed
▴ 30
0
votes
0
replies
913
views
Job:
Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData
RNA
DifferentialExpression
2.2 years ago
António Miguel de Jesus Domingues
▴ 510
0
votes
2
replies
988
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
2.2 years ago
sreekalasn
• 0
2
votes
1
reply
1.2k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 2.4 years ago by
Gordon Smyth
51k • written 2.4 years ago by
Mikołaj Mierzejewski
• 0
1
vote
2
replies
2.0k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
2.4 years ago
takemoto
• 0
1
vote
1
reply
928
views
Description of the headers obtained from the Eligos2 output
methylation
RNA
native
epitranscriptomics
updated 2.6 years ago by
tcalvo
▴ 100 • written 2.6 years ago by
megha.hs28
▴ 10
0
votes
1
reply
1.0k
views
Ensembl dataset version
tximport
rna
rnaseqGene
biomaRt
updated 2.8 years ago by
ATpoint
★ 4.5k • written 2.8 years ago by
st3472
• 0
0
votes
0
replies
765
views
Cross-cultivar RNA-seq analysis
RNA
Normalization
3.5 years ago
nancy
• 0
0
votes
4
replies
1.7k
views
Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma
edgeR
rna
3.5 years ago
Nirad
▴ 10
0
votes
3
replies
2.5k
views
Pearson correlation between gene expression and phenotype
edgeR
RNASeq
updated 3.9 years ago by
Gordon Smyth
51k • written 3.9 years ago by
weichengz
▴ 10
4
votes
3
replies
2.8k
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation
rna
updated 4.0 years ago by
James W. MacDonald
67k • written 4.0 years ago by
anthony.nash
▴ 20
2
votes
7
replies
1.4k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy
rna
hta2.0
r
updated 4.4 years ago by
James W. MacDonald
67k • written 4.4 years ago by
Marco_aurelio
• 0
1
vote
1
reply
946
views
How to interpret coefficients of time course modeled data with DESeq2?
deseq2
RNA
updated 4.5 years ago by
Michael Love
42k • written 4.5 years ago by
agsousa
• 0
0
votes
6
replies
1.6k
views
Bizarre Dispersion Plots
deseq2
RNA
RNASeq
updated 4.6 years ago by
Michael Love
42k • written 4.6 years ago by
stephen.hartley
• 0
0
votes
0
replies
945
views
Job:
Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell
RNA
Data analysis
Bioinformatics
Job
5.3 years ago
jmaanaki
• 0
1
vote
1
reply
1.6k
views
how to filter genes in significant module?
RNA
WGCNA
filter
5.3 years ago
modarzi
▴ 10
0
votes
2
replies
993
views
DESeq and checkFullRank(modelMatrix)
RNA
DESeq2
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
Merlin
▴ 10
2
votes
1
reply
919
views
DESeq2 statistic and design
deseq2
RNA
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
Merlin
▴ 10
5
votes
5
replies
1.6k
views
Association analysis between gene expression and Phenotype
rna
singlecell
limma
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
hrishi27n
▴ 20
2
votes
3
replies
1.5k
views
Number and percent of mapped reads from RNA seq analysis.
rna-seq
rna
updated 5.6 years ago by
Steve Lianoglou
★ 13k • written 5.6 years ago by
Anthony Nash
▴ 20
1
vote
0
replies
1.1k
views
Job:
1 Computational Biologist and 1 Molecular Biologist
computational biology
molecular biology
RNA
r-loop
ncRNA
Job
6.0 years ago
l.brown
▴ 10
0
votes
0
replies
1.1k
views
R code for finding wobble/redundant positions in an RNA string
r
code
rna
wobble
6.7 years ago
fawazfebin
▴ 60
0
votes
1
reply
1.1k
views
Time series comparison with DESEQ2
RNA
rnaseq
deseq2
updated 7.2 years ago by
Michael Love
42k • written 7.2 years ago by
hrishi27n
▴ 20
0
votes
1
reply
1.5k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2
RNA
rnaseq
updated 7.2 years ago by
Michael Love
42k • written 7.2 years ago by
hrishi27n
▴ 20
1
vote
1
reply
1.7k
views
Outliers - to remove or to not remove that is the question
outliers
rna
microarray
updated 7.4 years ago by
chris86
▴ 420 • written 7.4 years ago by
bhgyu
▴ 30
5
votes
4
replies
1.4k
views
Experiment design contrasts any time edgeR
DGE
rnaseq
RNA
edger
updated 7.5 years ago by
londonflavido
• 0 • written 7.5 years ago by
Pietro
▴ 40
3
votes
6
replies
2.1k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA
rna-seq
science
bioinformatics
updated 7.5 years ago by
James W. MacDonald
67k • written 7.5 years ago by
hrishi27n
▴ 20
6
votes
5
replies
4.2k
views
Clustering differential expression results from voomWithQualityWeights
RNA
limma
rsem
edgeR
updated 7.5 years ago by
Gordon Smyth
51k • written 7.5 years ago by
hrishi27n
▴ 20
0
votes
0
replies
1.7k
views
Finding candidate binding sites for RNA binding proteins in R
R
bioconductor
RNA
mRNA
RNA binding proteins
7.6 years ago
Walter F. Baumann
▴ 10
3
votes
1
reply
1.8k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR
deseq2
RNA
differential expression
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
tyssowski
• 0
0
votes
4
replies
5.2k
views
RNAseq Adjusting for Covariates?
RNA
rnaseq
Covariate
adjustment
deseq
updated 8.7 years ago by
Michael Love
42k • written 8.7 years ago by
sjs0282
• 0
0
votes
2
replies
1.4k
views
Normalizzation indipentent data from RNAAeq experiment
rna
normalization
10.1 years ago
aristotele_m
▴ 40
38 results • Page
1 of 1
Recent ...
Replies
Answer: Analysis of 2*4 factorial design
by
Gordon Smyth
51k
This is covered by Section 9.5 of the limma User's Guide. The analysis with a single-factor is much better. Your definition of A2 vs A1 …
Comment: Zero intra-block correlation in RRBS analysis using voomLmFit with block
by
Gordon Smyth
51k
It might be ok to estimate the intrablock correlation from the M-values. But then, if you do that, you may as well do the whole analysis in…
Answer: limma technical repeat correction
by
Gordon Smyth
51k
The technical samples should be averaged. Then use duplicateCorrelation() with block=PatientID.
Comment: New to mass spec data analysis
by
abhisek001
• 0
Thanks for your kind responses.
Comment: Duplicate row.names when building SummarizedExperiment with make_se in DEP
by
Anni
• 0
I encountered the same problem. Problem seems to be "make_se()" function that does *not* use variable 'label' to bind colData to assay, but…
Votes
Differential expression analysis starting from TPM data
Answer: How to identify top most variable genes from log2 normalized data?
Answer: How to identify top most variable genes from log2 normalized data?
Answer: clusterProfiler enrichGO on only T-cell related GO terms
Answer: clusterProfiler enrichGO on only T-cell related GO terms
Awards
• All
Popular Question
to
Bioinformagician
• 0
Teacher
to
Gordon Smyth
51k
Scholar
to
James W. MacDonald
67k
Teacher
to
Peter Langfelder
★ 3.0k
Popular Question
to
Assa Yeroslaviz
★ 1.5k
Locations
• All
France,
8 minutes ago
United States,
12 minutes ago
United States,
15 minutes ago
India,
44 minutes ago
Ireland,
44 minutes ago
Traffic: 496 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