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RNA Seq
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0
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9
replies
3.2k
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How to create manhattan plot with DESeq2
deseq2
mahattan plot
RNA Seq
updated 4.1 years ago by
bernatgel
▴ 150 • written 5.1 years ago by
adeler001
• 0
2
votes
5
replies
3.8k
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 4.6 years ago by
Steve Lianoglou
★ 13k • written 4.6 years ago by
svlachavas
▴ 830
0
votes
3
replies
906
views
Normalization of RNA seq data
RNA seq
cpm
updated 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 years ago by
isabel.pieterse
• 0
4
votes
4
replies
1.1k
views
Custom gene annotations for SGSeq
sgseq
alternative splicing
rna seq
updated 3 months ago by
Sara
• 0 • written 5.0 years ago by
116100016
• 0
1
vote
4
replies
1.1k
views
Difference between Fold Changes from EdgeR glmLRTest and directly calculated fold changes.
edger
RNA Seq
updated 5.0 years ago by
James W. MacDonald
67k • written 5.0 years ago by
abf
▴ 30
0
votes
0
replies
643
views
searching for specific RNA sequences
rna seq
5.0 years ago
adeler001
• 0
0
votes
2
replies
964
views
using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq
SGSeq
Alternative splicing
updated 5.1 years ago by
Leonard Goldstein
▴ 260 • written 5.1 years ago by
116100016
• 0
0
votes
1
reply
666
views
51 views DESeq2 RNAseq differential expression analysis
deseq2
likelihood ratio
rna seq
wald test
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
adeler001
• 0
0
votes
2
replies
1.1k
views
Need help cprrecting overlappinge genes on valcano plot
volcano plot
rna seq
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
adeler001
• 0
1
vote
5
replies
1.5k
views
Time course experiment using limma with voom
limma
voom
RNA Seq
Time-course experiments
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
mahes.muniandy
• 0
5
votes
3
replies
1.2k
views
Steep dendrograms and few modules. WGCNA on RNA seq data
RNA seq
wgcna
updated 5.5 years ago by
Peter Langfelder
★ 3.0k • written 5.5 years ago by
agustin.gonvi
▴ 20
1
vote
2
replies
2.2k
views
adapter trimming paired vs unpaired reads
rna seq
trimmomatic
trimming
adapter trimming
paired analysis
5.6 years ago
Mozart
▴ 30
0
votes
0
replies
1.8k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2
hierarchical clustering
microarray
RNA seq
DEG
6.8 years ago
lawarde.ankita1
▴ 30
13 results • Page
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Replies
Answer: Deseq2 res Function
by
Michael Love
43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR
by
Gordon Smyth
51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data
by
Gordon Smyth
51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix?
by
NB
• 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix?
by
James W. MacDonald
67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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