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RNA Seq
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0
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9
replies
2.5k
views
How to create manhattan plot with DESeq2
deseq2
mahattan plot
RNA Seq
updated 3.4 years ago by
bernatgel
▴ 150 • written 4.4 years ago by
adeler001
• 0
2
votes
5
replies
3.1k
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 3.9 years ago by
Steve Lianoglou
★ 13k • written 3.9 years ago by
svlachavas
▴ 830
0
votes
3
replies
626
views
Normalization of RNA seq data
RNA seq
cpm
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
isabel.pieterse
• 0
3
votes
3
replies
838
views
Custom gene annotations for SGSeq
sgseq
alternative splicing
rna seq
updated 4.3 years ago by
Leonard Goldstein
▴ 150 • written 4.3 years ago by
116100016
• 0
1
vote
4
replies
859
views
Difference between Fold Changes from EdgeR glmLRTest and directly calculated fold changes.
edger
RNA Seq
updated 4.3 years ago by
James W. MacDonald
65k • written 4.3 years ago by
abf
▴ 30
0
votes
0
replies
470
views
searching for specific RNA sequences
rna seq
4.4 years ago
adeler001
• 0
0
votes
2
replies
744
views
using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq
SGSeq
Alternative splicing
updated 4.4 years ago by
Leonard Goldstein
▴ 150 • written 4.4 years ago by
116100016
• 0
0
votes
1
reply
532
views
51 views DESeq2 RNAseq differential expression analysis
deseq2
likelihood ratio
rna seq
wald test
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
adeler001
• 0
0
votes
2
replies
916
views
Need help cprrecting overlappinge genes on valcano plot
volcano plot
rna seq
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
adeler001
• 0
1
vote
5
replies
1.2k
views
Time course experiment using limma with voom
limma
voom
RNA Seq
Time-course experiments
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
mahes.muniandy
• 0
5
votes
3
replies
891
views
Steep dendrograms and few modules. WGCNA on RNA seq data
RNA seq
wgcna
updated 4.8 years ago by
Peter Langfelder
★ 2.9k • written 4.8 years ago by
agustin.gonvi
▴ 20
1
vote
2
replies
1.8k
views
adapter trimming paired vs unpaired reads
rna seq
trimmomatic
trimming
adapter trimming
paired analysis
4.9 years ago
Mozart
▴ 30
0
votes
0
replies
1.6k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2
hierarchical clustering
microarray
RNA seq
DEG
6.1 years ago
lawarde.ankita1
▴ 30
13 results • Page
1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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