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RNA seq
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0
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9
replies
3.5k
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How to create manhattan plot with DESeq2
deseq2
mahattan plot
RNA Seq
updated 4.4 years ago by
bernatgel
▴ 150 • written 5.4 years ago by
adeler001
• 0
2
votes
5
replies
4.1k
views
Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
batch effect
limma
rna seq
DE
updated 4.9 years ago by
Steve Lianoglou
★ 13k • written 4.9 years ago by
svlachavas
▴ 840
0
votes
3
replies
1.1k
views
Normalization of RNA seq data
RNA seq
cpm
updated 4.9 years ago by
Kevin Blighe
★ 4.0k • written 4.9 years ago by
isabel.pieterse
• 0
4
votes
4
replies
1.2k
views
Custom gene annotations for SGSeq
sgseq
alternative splicing
rna seq
updated 7 months ago by
Sara
• 0 • written 5.3 years ago by
116100016
• 0
1
vote
4
replies
1.2k
views
Difference between Fold Changes from EdgeR glmLRTest and directly calculated fold changes.
edger
RNA Seq
updated 5.3 years ago by
James W. MacDonald
68k • written 5.3 years ago by
abf
▴ 30
0
votes
0
replies
687
views
searching for specific RNA sequences
rna seq
5.3 years ago
adeler001
• 0
0
votes
2
replies
1.1k
views
using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq
SGSeq
Alternative splicing
updated 5.4 years ago by
Leonard Goldstein
▴ 260 • written 5.4 years ago by
116100016
• 0
0
votes
1
reply
711
views
51 views DESeq2 RNAseq differential expression analysis
deseq2
likelihood ratio
rna seq
wald test
updated 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
adeler001
• 0
0
votes
2
replies
1.2k
views
Need help cprrecting overlappinge genes on valcano plot
volcano plot
rna seq
updated 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
adeler001
• 0
1
vote
5
replies
1.6k
views
Time course experiment using limma with voom
limma
voom
RNA Seq
Time-course experiments
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
mahes.muniandy
• 0
5
votes
3
replies
1.4k
views
Steep dendrograms and few modules. WGCNA on RNA seq data
RNA seq
wgcna
updated 5.8 years ago by
Peter Langfelder
★ 3.0k • written 5.8 years ago by
agustin.gonvi
▴ 20
1
vote
2
replies
2.4k
views
adapter trimming paired vs unpaired reads
rna seq
trimmomatic
trimming
adapter trimming
paired analysis
5.8 years ago
Mozart
▴ 30
0
votes
0
replies
1.9k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2
hierarchical clustering
microarray
RNA seq
DEG
7.1 years ago
lawarde.ankita1
▴ 30
13 results • Page
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Answer: Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
by
James W. MacDonald
68k
As an example ``` > library(GEOquery) > library(oligo) > library(limma) > library(affycoretools) ## you need this package to annota…
Comment: EuroBioC2023 abstract submission is open!
by
ht
• 0
Great news about EuroBioC2023 abstract submissions! This is an excellent opportunity to share cutting-edge research. Speaking of cutting-ed…
Comment: orgDB
by
shepherl
4.1k
You should look at the documentation on the help pages for those packages. It should be clear enough there. But to speed things along: `…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to
by
Harry
• 0
It's interesting to see how the normalization factors are all 1, yet the MA plot reflects changes, indicating that the normalization proces…
Comment: European Bioconductor Conference 2023 planning
by
Andrew
• 0
Great information! This is a great opportunity for the computational biology community to connect and grow. @[Chill Guy Clicker][1] [1…
Votes
Calculating TOM in blockwise WGCNA
A: What is the "linear model" part used for in Limma?
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
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