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rna seq
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0
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9
replies
4.1k
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How to create manhattan plot with DESeq2
deseq2
mahattan plot
RNA Seq
updated 5.2 years ago by
bernatgel
▴ 150 • written 6.2 years ago by
adeler001
• 0
2
votes
5
replies
5.0k
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 5.7 years ago by
Steve Lianoglou
★ 13k • written 5.7 years ago by
svlachavas
▴ 840
0
votes
3
replies
1.5k
views
Normalization of RNA seq data
RNA seq
cpm
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
isabel.pieterse
• 0
4
votes
4
replies
1.5k
views
Custom gene annotations for SGSeq
sgseq
alternative splicing
rna seq
updated 16 months ago by
Sara
• 0 • written 6.1 years ago by
116100016
• 0
1
vote
4
replies
1.4k
views
Difference between Fold Changes from EdgeR glmLRTest and directly calculated fold changes.
edger
RNA Seq
updated 6.1 years ago by
James W. MacDonald
68k • written 6.1 years ago by
abf
▴ 30
0
votes
0
replies
836
views
searching for specific RNA sequences
rna seq
6.1 years ago
adeler001
• 0
0
votes
2
replies
1.4k
views
using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq
SGSeq
Alternative splicing
updated 6.2 years ago by
Leonard Goldstein
▴ 260 • written 6.2 years ago by
116100016
• 0
0
votes
1
reply
855
views
51 views DESeq2 RNAseq differential expression analysis
deseq2
likelihood ratio
rna seq
wald test
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
adeler001
• 0
0
votes
2
replies
1.5k
views
Need help cprrecting overlappinge genes on valcano plot
volcano plot
rna seq
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
adeler001
• 0
1
vote
5
replies
2.0k
views
Time course experiment using limma with voom
limma
voom
RNA Seq
Time-course experiments
updated 6.5 years ago by
Aaron Lun
★ 29k • written 6.5 years ago by
mahes.muniandy
• 0
5
votes
3
replies
1.7k
views
Steep dendrograms and few modules. WGCNA on RNA seq data
RNA seq
wgcna
updated 6.6 years ago by
Peter Langfelder
★ 3.0k • written 6.6 years ago by
agustin.gonvi
▴ 20
1
vote
2
replies
2.8k
views
adapter trimming paired vs unpaired reads
rna seq
trimmomatic
trimming
adapter trimming
paired analysis
6.6 years ago
Mozart
▴ 30
0
votes
0
replies
2.2k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2
hierarchical clustering
microarray
RNA seq
DEG
7.8 years ago
lawarde.ankita1
▴ 30
13 results • Page
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Answer: segfault in edgeR glmQLFit
by
Gordon Smyth
53k
Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. We will …
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
aqeel
• 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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