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rnaseqr
•
reset
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 7 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
1
vote
10
replies
2.9k
views
Duplicate correlation with limma in before-after exposure experiment
RNASeqR
3.4 years ago • updated 3.0 years ago
sofie.haglund
• 0
7
votes
6
replies
3.4k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2
R
RNASeqR
3.4 years ago
ecg1g15
▴ 20
3
votes
5
replies
2.1k
views
Volcano plot - select additional gene
EnhancedVolcano
RNASeqR
R
volcanoplot
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 years ago by
camillab.
▴ 10
5
votes
5
replies
2.5k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
H. Z. Amini
▴ 10
1
vote
5
replies
1.6k
views
while designing matrix i got an error, please help me out
RNASeqR
updated 3.1 years ago by
Basti
▴ 780 • written 3.1 years ago by
Rishav
▴ 20
1
vote
5
replies
882
views
Error when calculating DE using the classical approach in edgeR
RNASeqR
3.1 years ago
Rishav
▴ 20
3
votes
4
replies
1.4k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.1 years ago
hgalmoore
• 0
0
votes
3
replies
1.3k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 20 months ago by
ATpoint
★ 4.1k • written 20 months ago by
fatemehfakhari74
• 0
1
vote
3
replies
1.2k
views
Error with hclust
RNASeqR
#hclust
#wgcna
#dissimilarity
#average
updated 2.4 years ago by
ATpoint
★ 4.1k • written 2.4 years ago by
devbhavin20
• 0
1
vote
3
replies
904
views
Need help in doing network analysis using R
RNASeqR
updated 3.1 years ago by
ATpoint
★ 4.1k • written 3.1 years ago by
Rishav
▴ 20
1
vote
3
replies
1.7k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData
RNASeq
RNASeqR
3.0 years ago
dantasezequiel1
• 0
0
votes
2
replies
2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 8 months ago by
manuel.fernandez
• 0 • written 2.1 years ago by
cicely.day
• 0
0
votes
2
replies
5.3k
views
TPM data in limma/voom
voom
limma
DifferentialExpression
edgeR
3.2 years ago
RJM
• 0
1
vote
2
replies
1.4k
views
I am creating contrast matrix and i am following every procedure but still i don't understand where i am getting error
RNASeqR
3.1 years ago
Rishav
▴ 20
1
vote
2
replies
839
views
Error occured in designing a matrix
RNASeqR
updated 3.1 years ago by
Gordon Smyth
50k • written 3.1 years ago by
Rishav
▴ 20
1
vote
2
replies
836
views
Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 3.1 years ago by
Gordon Smyth
50k • written 3.1 years ago by
Rishav
▴ 20
2
votes
2
replies
1.5k
views
Need help in determing upregulated and downregulated genes
RNASeqR
3.0 years ago
Rishav
▴ 20
0
votes
1
reply
2.3k
views
Biological replicates in DESeq2
DESeq2
Bioconductor
RNASeqR
updated 3.2 years ago by
ATpoint
★ 4.1k • written 3.2 years ago by
Blanca
• 0
0
votes
1
reply
838
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data
RNASeqR
Normalization
BatchEffect
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
bhandary.8590
▴ 20
0
votes
1
reply
921
views
Outliers on DESEq2 Results
RNASeqR
DifferentialExpression
DESeq2
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
Bruno Rodrigo
• 0
4
votes
1
reply
2.0k
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene
RNASeqR
DESeq2
RNAseq
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
sohail.mbio
▴ 10
0
votes
1
reply
750
views
Find significant genes related to a specific disease
GeneExpression
RNASeqR
limma
updated 3.4 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 3.4 years ago by
Will
• 0
1
vote
1
reply
787
views
edgeR for SDE analysis
RNASeqRData
edgeR
RNASeqR
RNASeqData
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
vikycairoli
• 0
0
votes
1
reply
972
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 20 months ago by
Michael Love
41k • written 20 months ago by
estafana.t98
• 0
0
votes
1
reply
1.0k
views
Using tximport to create the input for DESeq2
RNASeqR
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
ahmesalama
• 0
0
votes
1
reply
866
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData
limma
RNASeq
RNASeqR
updated 3.1 years ago by
Gordon Smyth
50k • written 3.1 years ago by
Rita
• 0
27 results • Page
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Replies
Comment: Couldn't connect to server while using "pathways"
by
ATpoint
★ 4.1k
Please understand that we neither can see your screen, nor read minds. You at least need to provide the line of code and the name of the pa…
Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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