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rnaseqr
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6
votes
11
replies
3.7k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 17 days ago by
Priya
• 0 • written 3.1 years ago by
Marina
▴ 40
0
votes
2
replies
2.1k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 7 months ago by
manuel.fernandez
• 0 • written 23 months ago by
cicely.day
• 0
0
votes
1
reply
911
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 19 months ago by
Michael Love
41k • written 19 months ago by
estafana.t98
• 0
0
votes
3
replies
1.2k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 19 months ago by
ATpoint
★ 4.0k • written 19 months ago by
fatemehfakhari74
• 0
1
vote
1
reply
759
views
edgeR for SDE analysis
RNASeqRData
edgeR
RNASeqR
RNASeqData
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
vikycairoli
• 0
1
vote
3
replies
1.1k
views
Error with hclust
RNASeqR
#hclust
#wgcna
#dissimilarity
#average
updated 2.3 years ago by
ATpoint
★ 4.0k • written 2.3 years ago by
devbhavin20
• 0
4
votes
1
reply
1.9k
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene
RNASeqR
DESeq2
RNAseq
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
sohail.mbio
▴ 10
0
votes
1
reply
808
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data
RNASeqR
Normalization
BatchEffect
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
bhandary.8590
▴ 20
0
votes
1
reply
891
views
Outliers on DESEq2 Results
RNASeqR
DifferentialExpression
DESeq2
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
Bruno Rodrigo
• 0
1
vote
10
replies
2.8k
views
Duplicate correlation with limma in before-after exposure experiment
RNASeqR
3.3 years ago • updated 2.9 years ago
sofie.haglund
• 0
2
votes
2
replies
1.4k
views
Need help in determing upregulated and downregulated genes
RNASeqR
2.9 years ago
Rishav
▴ 20
1
vote
3
replies
1.6k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData
RNASeq
RNASeqR
2.9 years ago
dantasezequiel1
• 0
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.0 years ago
hgalmoore
• 0
0
votes
1
reply
842
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData
limma
RNASeq
RNASeqR
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Rita
• 0
1
vote
5
replies
1.5k
views
while designing matrix i got an error, please help me out
RNASeqR
updated 3.0 years ago by
Basti
▴ 750 • written 3.0 years ago by
Rishav
▴ 20
1
vote
2
replies
807
views
Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Rishav
▴ 20
1
vote
3
replies
840
views
Need help in doing network analysis using R
RNASeqR
updated 3.0 years ago by
ATpoint
★ 4.0k • written 3.0 years ago by
Rishav
▴ 20
1
vote
2
replies
807
views
Error occured in designing a matrix
RNASeqR
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Rishav
▴ 20
1
vote
5
replies
835
views
Error when calculating DE using the classical approach in edgeR
RNASeqR
3.0 years ago
Rishav
▴ 20
1
vote
2
replies
1.3k
views
I am creating contrast matrix and i am following every procedure but still i don't understand where i am getting error
RNASeqR
3.0 years ago
Rishav
▴ 20
0
votes
1
reply
2.2k
views
Biological replicates in DESeq2
DESeq2
Bioconductor
RNASeqR
updated 3.1 years ago by
ATpoint
★ 4.0k • written 3.1 years ago by
Blanca
• 0
0
votes
1
reply
1.0k
views
Using tximport to create the input for DESeq2
RNASeqR
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
ahmesalama
• 0
5
votes
5
replies
2.4k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
updated 3.1 years ago by
James W. MacDonald
65k • written 3.1 years ago by
H. Z. Amini
▴ 10
0
votes
2
replies
5.0k
views
TPM data in limma/voom
voom
limma
DifferentialExpression
edgeR
3.1 years ago
RJM
• 0
0
votes
1
reply
727
views
Find significant genes related to a specific disease
GeneExpression
RNASeqR
limma
updated 3.3 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 3.3 years ago by
Will
• 0
7
votes
6
replies
3.3k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2
R
RNASeqR
3.3 years ago
ecg1g15
▴ 20
3
votes
5
replies
2.0k
views
Volcano plot - select additional gene
EnhancedVolcano
RNASeqR
R
volcanoplot
updated 3.4 years ago by
Kevin Blighe
★ 3.9k • written 3.4 years ago by
camillab.
▴ 10
27 results • Page
1 of 1
Recent ...
Replies
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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