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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 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
hrishi27n
▴ 20
5
votes
4
replies
1.3k
views
Experiment design contrasts any time edgeR
DGE
rnaseq
RNA
edger
updated 6.9 years ago by
londonflavido
• 0 • written 6.9 years ago by
Pietro
▴ 40
4
votes
3
replies
2.1k
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 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 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 6.9 years ago by
James W. MacDonald
65k • written 6.9 years ago by
hrishi27n
▴ 20
3
votes
6
replies
1.8k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2
edgeR
RNA
limma
Normalization
16 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 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
Marco_aurelio
• 0
2
votes
1
reply
966
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
Mikołaj Mierzejewski
• 0
2
votes
1
reply
799
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 5.0 years ago by
Steve Lianoglou
★ 13k • written 5.0 years ago by
Anthony Nash
▴ 20
1
vote
1
reply
643
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 18 months ago by
ATpoint
★ 4.0k • written 18 months ago by
Mohamed
▴ 30
1
vote
1
reply
1.3k
views
how to filter genes in significant module?
RNA
WGCNA
filter
4.7 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 6.8 years ago by
chris86
▴ 420 • written 6.8 years ago by
bhgyu
▴ 30
1
vote
0
replies
915
views
Job:
1 Computational Biologist and 1 Molecular Biologist
computational biology
molecular biology
RNA
r-loop
ncRNA
Job
5.4 years ago
l.brown
▴ 10
1
vote
1
reply
754
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
752
views
How to interpret coefficients of time course modeled data with DESeq2?
deseq2
RNA
updated 3.9 years ago by
Michael Love
41k • written 3.9 years ago by
agsousa
• 0
1
vote
2
replies
1.5k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
22 months ago
takemoto
• 0
0
votes
2
replies
1.3k
views
Normalizzation indipentent data from RNAAeq experiment
rna
normalization
9.5 years ago
aristotele_m
▴ 40
0
votes
2
replies
967
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt
ensembldb
RNA
ensembl
updated 11 months ago by
Johannes Rainer
★ 2.0k • written 12 months ago by
Christopher
• 0
0
votes
4
replies
4.9k
views
RNAseq Adjusting for Covariates?
RNA
rnaseq
Covariate
adjustment
deseq
updated 8.1 years ago by
Michael Love
41k • written 8.1 years ago by
sjs0282
• 0
0
votes
0
replies
1.4k
views
Finding candidate binding sites for RNA binding proteins in R
R
bioconductor
RNA
mRNA
RNA binding proteins
7.0 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
942
views
Time series comparison with DESEQ2
RNA
rnaseq
deseq2
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
hrishi27n
▴ 20
0
votes
0
replies
908
views
R code for finding wobble/redundant positions in an RNA string
r
code
rna
wobble
6.1 years ago
fawazfebin
▴ 60
0
votes
2
replies
856
views
DESeq and checkFullRank(modelMatrix)
RNA
DESeq2
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
Merlin
▴ 10
0
votes
0
replies
787
views
Job:
Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell
RNA
Data analysis
Bioinformatics
Job
4.7 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
2.1k
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
225
views
Running Deseq2 with all samples vs samples for each comparison separately
RNA
DESeq2
updated 9 weeks ago by
Michael Love
41k • written 9 weeks ago by
manuel
• 0
0
votes
2
replies
793
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
20 months ago • updated 19 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
494
views
Correct GFF3 translation for FeatureCounts
RNASeq
FeatureCounts
Rna
17 months ago
rridley3
• 0
0
votes
0
replies
717
views
Job:
Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData
RNA
DifferentialExpression
19 months ago
António Miguel de Jesus Domingues
▴ 490
0
votes
0
replies
564
views
Cross-cultivar RNA-seq analysis
RNA
Normalization
2.9 years ago
nancy
• 0
0
votes
1
reply
839
views
Ensembl dataset version
tximport
rna
rnaseqGene
biomaRt
updated 2.2 years ago by
ATpoint
★ 4.0k • written 2.2 years ago by
st3472
• 0
0
votes
5
replies
347
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 6 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
Gordon
• 0
37 results • Page
1 of 1
Recent ...
Replies
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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