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RNA Seq
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0
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9
replies
1.3k
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How to create manhattan plot with DESeq2
deseq2
mahattan plot
RNA Seq
updated 22 months ago by
bernatgel
▴ 140 • written 2.8 years ago by
adeler001
• 0
2
votes
5
replies
1.3k
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 2.3 years ago by
Steve Lianoglou
13k • written 2.3 years ago by
svlachavas
▴ 800
0
votes
3
replies
287
views
Normalization of RNA seq data
RNA seq
cpm
updated 2.3 years ago by
Kevin Blighe
3.6k • written 2.3 years ago by
isabel.pieterse
• 0
3
votes
3
replies
378
views
Custom gene annotations for SGSeq
sgseq
alternative splicing
rna seq
updated 2.7 years ago by
Leonard Goldstein
▴ 110 • written 2.7 years ago by
116100016
• 0
1
vote
4
replies
354
views
Difference between Fold Changes from EdgeR glmLRTest and directly calculated fold changes.
edger
RNA Seq
updated 2.7 years ago by
James W. MacDonald
60k • written 2.7 years ago by
abf
▴ 30
0
votes
0
replies
222
views
searching for specific RNA sequences
rna seq
2.7 years ago
adeler001
• 0
0
votes
2
replies
353
views
using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq
SGSeq
Alternative splicing
updated 2.8 years ago by
Leonard Goldstein
▴ 110 • written 2.8 years ago by
116100016
• 0
0
votes
1
reply
262
views
51 views DESeq2 RNAseq differential expression analysis
deseq2
likelihood ratio
rna seq
wald test
updated 2.9 years ago by
Michael Love
37k • written 2.9 years ago by
adeler001
• 0
0
votes
2
replies
467
views
Need help cprrecting overlappinge genes on valcano plot
volcano plot
rna seq
updated 3.0 years ago by
Michael Love
37k • written 3.0 years ago by
adeler001
• 0
1
vote
5
replies
604
views
Time course experiment using limma with voom
limma
voom
RNA Seq
Time-course experiments
updated 3.2 years ago by
Aaron Lun
★ 27k • written 3.2 years ago by
mahes.muniandy
• 0
5
votes
3
replies
482
views
Steep dendrograms and few modules. WGCNA on RNA seq data
RNA seq
wgcna
updated 3.2 years ago by
Peter Langfelder
★ 2.7k • written 3.2 years ago by
agustin.gonvi
▴ 10
1
vote
2
replies
1.0k
views
adapter trimming paired vs unpaired reads
rna seq
trimmomatic
trimming
adapter trimming
paired analysis
3.3 years ago
Mozart
▴ 20
0
votes
0
replies
1.1k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2
hierarchical clustering
microarray
RNA seq
DEG
4.5 years ago
lawarde.ankita1
▴ 20
13 results • Page
1 of 1
Recent ...
Replies
Comment: using DESeq2 for ATAC analyses
by
eric.kern13
▴ 10
To expand on what's written here: deseq2 can achieve roughly constant variance $C$ across genes by setting the per-gene dispersion $\phi_j$…
Comment: TPM normalization starting with read counts
by
ATpoint
★ 1.4k
Neither edgeR nor DESeq2 output TPM directly. TPM is easy to calculate though if counts and appropriate length info is available (https://s…
Comment: error running UniProt.ws
by
davi.vuko
• 0
I still get the same result as above, should running BiocManager::install() do the trick?
Answer: Adding custom transcript to Salmon index
by
ATpoint
★ 1.4k
Yes, you would add the sequence to the reference transcriptome that is used for the gentrome construction. Simply make a separate fasta fil…
Comment: IsoformSwitchAnalyzeR package on mouse data
by
bpshtiwan
▴ 10
Hello Ryan, Also, I am not able to find esemble file that has haplotype info in it. Kindly, have you solved the problem? Best
Votes
A: Importance of Order in Design Formula
remove microarray batch effects using Limma
On empirical Bayes of edgeR
Answer: CQN to DESeq2
Comment: package 'BiocInstaller' is not available (for R version 3.4.4)
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