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Rna
•
reset
0
votes
3
replies
351
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Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA
RNASeqPower
DEGseq
written 3 months ago by
Jonathan
• 0
0
votes
3
replies
646
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO
rnaseqGene
RNA
7 months ago
gallantk5
• 0
0
votes
5
replies
1.3k
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
Gordon
• 0
0
votes
1
reply
661
views
Running Deseq2 with all samples vs samples for each comparison separately
RNA
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
manuel
• 0
0
votes
2
replies
1.7k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt
ensembldb
RNA
ensembl
updated 23 months ago by
Johannes Rainer
★ 2.1k • written 23 months ago by
Christopher
• 0
3
votes
6
replies
2.9k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2
edgeR
RNA
limma
Normalization
2.3 years ago
Sara
• 0
0
votes
0
replies
745
views
Correct GFF3 translation for FeatureCounts
RNASeq
FeatureCounts
Rna
2.4 years ago
rridley3
• 0
1
vote
1
reply
1.0k
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 2.5 years ago by
ATpoint
★ 4.7k • written 2.5 years ago by
Mohamed
▴ 30
0
votes
0
replies
983
views
Job:
Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData
RNA
DifferentialExpression
2.5 years ago
António Miguel de Jesus Domingues
▴ 510
0
votes
2
replies
1.1k
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
2.6 years ago • updated 2.5 years ago
sreekalasn
• 0
2
votes
1
reply
1.4k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 2.7 years ago by
Gordon Smyth
52k • written 2.7 years ago by
Mikołaj Mierzejewski
• 0
1
vote
2
replies
2.2k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
2.8 years ago
takemoto
• 0
1
vote
1
reply
1.0k
views
Description of the headers obtained from the Eligos2 output
methylation
RNA
native
epitranscriptomics
updated 3.0 years ago by
tcalvo
▴ 100 • written 3.0 years ago by
megha.hs28
▴ 10
0
votes
1
reply
1.1k
views
Ensembl dataset version
tximport
rna
rnaseqGene
biomaRt
updated 3.2 years ago by
ATpoint
★ 4.7k • written 3.2 years ago by
st3472
• 0
0
votes
0
replies
833
views
Cross-cultivar RNA-seq analysis
RNA
Normalization
3.9 years ago
nancy
• 0
0
votes
4
replies
1.8k
views
Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma
edgeR
rna
3.9 years ago
Nirad
▴ 10
0
votes
3
replies
2.8k
views
Pearson correlation between gene expression and phenotype
edgeR
RNASeq
updated 4.3 years ago by
Gordon Smyth
52k • written 4.3 years ago by
weichengz
▴ 10
4
votes
3
replies
3.1k
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation
rna
updated 4.4 years ago by
James W. MacDonald
68k • written 4.4 years ago by
anthony.nash
▴ 20
2
votes
7
replies
1.6k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy
rna
hta2.0
r
updated 4.8 years ago by
James W. MacDonald
68k • written 4.8 years ago by
Marco_aurelio
• 0
1
vote
1
reply
1.0k
views
How to interpret coefficients of time course modeled data with DESeq2?
deseq2
RNA
updated 4.8 years ago by
Michael Love
43k • written 4.8 years ago by
agsousa
• 0
0
votes
6
replies
1.8k
views
Bizarre Dispersion Plots
deseq2
RNA
RNASeq
updated 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
stephen.hartley
• 0
0
votes
0
replies
1.1k
views
Job:
Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell
RNA
Data analysis
Bioinformatics
Job
5.6 years ago
jmaanaki
• 0
1
vote
1
reply
1.7k
views
how to filter genes in significant module?
RNA
WGCNA
filter
5.7 years ago
modarzi
▴ 10
0
votes
2
replies
1.1k
views
DESeq and checkFullRank(modelMatrix)
RNA
DESeq2
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
Merlin
▴ 10
2
votes
1
reply
1.0k
views
DESeq2 statistic and design
deseq2
RNA
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
Merlin
▴ 10
5
votes
5
replies
1.8k
views
Association analysis between gene expression and Phenotype
rna
singlecell
limma
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
hrishi27n
▴ 20
2
votes
3
replies
1.8k
views
Number and percent of mapped reads from RNA seq analysis.
rna-seq
rna
updated 5.9 years ago by
Steve Lianoglou
★ 13k • written 5.9 years ago by
Anthony Nash
▴ 20
1
vote
0
replies
1.2k
views
Job:
1 Computational Biologist and 1 Molecular Biologist
computational biology
molecular biology
RNA
r-loop
ncRNA
Job
6.4 years ago
l.brown
▴ 10
0
votes
0
replies
1.2k
views
R code for finding wobble/redundant positions in an RNA string
r
code
rna
wobble
7.1 years ago
fawazfebin
▴ 60
0
votes
1
reply
1.2k
views
Time series comparison with DESEQ2
RNA
rnaseq
deseq2
updated 7.5 years ago by
Michael Love
43k • written 7.5 years ago by
hrishi27n
▴ 20
0
votes
1
reply
1.6k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2
RNA
rnaseq
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
hrishi27n
▴ 20
1
vote
1
reply
2.1k
views
Outliers - to remove or to not remove that is the question
outliers
rna
microarray
updated 7.8 years ago by
chris86
▴ 420 • written 7.8 years ago by
bhgyu
▴ 30
5
votes
4
replies
1.6k
views
Experiment design contrasts any time edgeR
DGE
rnaseq
RNA
edger
updated 7.8 years ago by
londonflavido
• 0 • written 7.8 years ago by
Pietro
▴ 40
3
votes
6
replies
2.2k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA
rna-seq
science
bioinformatics
updated 7.9 years ago by
James W. MacDonald
68k • written 7.9 years ago by
hrishi27n
▴ 20
6
votes
5
replies
4.5k
views
Clustering differential expression results from voomWithQualityWeights
RNA
limma
rsem
edgeR
updated 7.9 years ago by
Gordon Smyth
52k • written 7.9 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
8.0 years ago
Walter F. Baumann
▴ 10
3
votes
1
reply
1.9k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR
deseq2
RNA
differential expression
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
tyssowski
• 0
0
votes
4
replies
5.3k
views
RNAseq Adjusting for Covariates?
RNA
rnaseq
Covariate
adjustment
deseq
updated 9.0 years ago by
Michael Love
43k • written 9.0 years ago by
sjs0282
• 0
0
votes
2
replies
1.5k
views
Normalizzation indipentent data from RNAAeq experiment
rna
normalization
10.4 years ago
aristotele_m
▴ 40
39 results • Page
1 of 1
Recent ...
Replies
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to
by
ATpoint
★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Answer: how many significant figures are there in DESeq2 output
by
ATpoint
★ 4.7k
I strongly recommend to not concern yourself with these sorts of marginal problems because you're entering a realm in which you're entirely…
Comment: Problem using locateVariants() from the VariantAnnotation package
by
Marco
• 0
Ok, I think I found the problem. By looking at the `locateVariants()` source code, I was able to pinpoint that the problems is when trying …
Comment: Conumee for EPIC and EPICv2 copy number
by
Adam
• 0
As described on the [github](https://github.com/hovestadtlab/conumee2) the way to do this is using array_type = c("EPIC", "EPICv2") This i…
Comment: graper 1.22 Build is Broken
by
shepherl
4.1k
This is not an appropriate place to report this. this is for usage questions. maintainers are notified automatically when it is failing on …
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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