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
6
votes
5
replies
3.8k
views
Clustering differential expression results from voomWithQualityWeights
RNA
limma
rsem
edgeR
updated 7.0 years ago by
Gordon Smyth
50k • written 7.0 years ago by
hrishi27n
▴ 20
5
votes
5
replies
1.4k
views
Association analysis between gene expression and Phenotype
rna
singlecell
limma
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
hrishi27n
▴ 20
5
votes
4
replies
1.3k
views
Experiment design contrasts any time edgeR
DGE
rnaseq
RNA
edger
updated 7.0 years ago by
londonflavido
• 0 • written 7.0 years ago by
Pietro
▴ 40
4
votes
3
replies
2.2k
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation
rna
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
anthony.nash
▴ 20
3
votes
1
reply
1.6k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR
deseq2
RNA
differential expression
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
tyssowski
• 0
3
votes
6
replies
1.9k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA
rna-seq
science
bioinformatics
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
hrishi27n
▴ 20
3
votes
6
replies
1.9k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2
edgeR
RNA
limma
Normalization
17 months ago
Sara
• 0
2
votes
7
replies
1.2k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy
rna
hta2.0
r
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
Marco_aurelio
• 0
2
votes
1
reply
1000
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 22 months ago by
Gordon Smyth
50k • written 22 months ago by
Mikołaj Mierzejewski
• 0
2
votes
1
reply
813
views
DESeq2 statistic and design
deseq2
RNA
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
3
replies
1.1k
views
Number and percent of mapped reads from RNA seq analysis.
rna-seq
rna
updated 5.1 years ago by
Steve Lianoglou
★ 13k • written 5.1 years ago by
Anthony Nash
▴ 20
1
vote
1
reply
693
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 19 months ago by
ATpoint
★ 4.0k • written 19 months ago by
Mohamed
▴ 30
1
vote
1
reply
1.3k
views
how to filter genes in significant module?
RNA
WGCNA
filter
4.8 years ago
modarzi
▴ 10
1
vote
1
reply
1.3k
views
Outliers - to remove or to not remove that is the question
outliers
rna
microarray
updated 6.9 years ago by
chris86
▴ 420 • written 6.9 years ago by
bhgyu
▴ 30
1
vote
0
replies
932
views
Job:
1 Computational Biologist and 1 Molecular Biologist
computational biology
molecular biology
RNA
r-loop
ncRNA
Job
5.5 years ago
l.brown
▴ 10
1
vote
1
reply
775
views
Description of the headers obtained from the Eligos2 output
methylation
RNA
native
epitranscriptomics
updated 2.1 years ago by
tcalvo
▴ 90 • written 2.1 years ago by
megha.hs28
▴ 10
1
vote
1
reply
777
views
How to interpret coefficients of time course modeled data with DESeq2?
deseq2
RNA
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
agsousa
• 0
1
vote
2
replies
1.6k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
23 months ago
takemoto
• 0
0
votes
2
replies
1.3k
views
Normalizzation indipentent data from RNAAeq experiment
rna
normalization
9.6 years ago
aristotele_m
▴ 40
0
votes
2
replies
1.0k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt
ensembldb
RNA
ensembl
updated 12 months ago by
Johannes Rainer
★ 2.0k • written 12 months ago by
Christopher
• 0
0
votes
4
replies
5.0k
views
RNAseq Adjusting for Covariates?
RNA
rnaseq
Covariate
adjustment
deseq
updated 8.2 years ago by
Michael Love
41k • written 8.2 years ago by
sjs0282
• 0
0
votes
0
replies
1.5k
views
Finding candidate binding sites for RNA binding proteins in R
R
bioconductor
RNA
mRNA
RNA binding proteins
7.1 years ago
Walter F. Baumann
▴ 10
0
votes
1
reply
1.4k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2
RNA
rnaseq
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
hrishi27n
▴ 20
0
votes
1
reply
978
views
Time series comparison with DESEQ2
RNA
rnaseq
deseq2
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
hrishi27n
▴ 20
0
votes
0
replies
931
views
R code for finding wobble/redundant positions in an RNA string
r
code
rna
wobble
6.2 years ago
fawazfebin
▴ 60
0
votes
2
replies
878
views
DESeq and checkFullRank(modelMatrix)
RNA
DESeq2
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
0
replies
809
views
Job:
Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell
RNA
Data analysis
Bioinformatics
Job
4.8 years ago
jmaanaki
• 0
0
votes
6
replies
1.2k
views
Bizarre Dispersion Plots
deseq2
RNA
RNASeq
updated 4.1 years ago by
Michael Love
41k • written 4.1 years ago by
stephen.hartley
• 0
0
votes
3
replies
2.2k
views
Pearson correlation between gene expression and phenotype
edgeR
RNASeq
updated 3.4 years ago by
Gordon Smyth
50k • written 3.4 years ago by
weichengz
▴ 10
0
votes
1
reply
265
views
Running Deseq2 with all samples vs samples for each comparison separately
RNA
DESeq2
updated 3 months ago by
Michael Love
41k • written 3 months ago by
manuel
• 0
0
votes
2
replies
827
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
20 months ago
sreekalasn
• 0
0
votes
4
replies
1.3k
views
Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma
edgeR
rna
3.0 years ago
Nirad
▴ 10
0
votes
0
replies
522
views
Correct GFF3 translation for FeatureCounts
RNASeq
FeatureCounts
Rna
18 months ago
rridley3
• 0
0
votes
0
replies
763
views
Job:
Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData
RNA
DifferentialExpression
20 months ago
António Miguel de Jesus Domingues
▴ 490
0
votes
0
replies
584
views
Cross-cultivar RNA-seq analysis
RNA
Normalization
3.0 years ago
nancy
• 0
0
votes
1
reply
858
views
Ensembl dataset version
tximport
rna
rnaseqGene
biomaRt
updated 2.3 years ago by
ATpoint
★ 4.0k • written 2.3 years ago by
st3472
• 0
0
votes
5
replies
448
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 10 weeks ago by
James W. MacDonald
65k • written 11 weeks ago by
Gordon
• 0
37 results • Page
1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Awards
• All
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Supporter
to
Jonathan
▴ 10
Popular Question
to
Bine
▴ 40
Scholar
to
ATpoint
★ 4.0k
Locations
• All
France,
28 minutes ago
WEHI, Melbourne, Australia,
34 minutes ago
Melbourne, Australia,
1 hour ago
United States,
1 hour ago
Canada,
1 hour ago
Traffic: 745 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