Showing : rnaseqr • reset
1
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10
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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
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
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2.2k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 7 months ago by • 0 • written 2.0 years ago by • 0
0
votes
2
replies
5.2k
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
3.2 years ago RJM • 0
5
votes
5
replies
2.4k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Using tximport to create the input for DESeq2
RNASeqR
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
6
votes
11
replies
3.9k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 6 weeks ago by • 0 • written 3.2 years ago by ▴ 40
0
votes
1
reply
2.3k
views
Biological replicates in DESeq2
DESeq2 Bioconductor RNASeqR
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
1
vote
5
replies
875
views
Error when calculating DE using the classical approach in edgeR
RNASeqR
3.1 years ago Rishav ▴ 20
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
829
views
Error occured in designing a matrix
RNASeqR
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
1
vote
3
replies
880
views
Need help in doing network analysis using R
RNASeqR
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by ▴ 20
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
0
votes
1
reply
741
views
Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 3.4 years ago by ▴ 490 • written 3.4 years ago by • 0
0
votes
1
reply
857
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 3.1 years ago by 50k • written 3.1 years ago by • 0
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.1 years ago hgalmoore • 0
1
vote
3
replies
1.2k
views
Error with hclust
RNASeqR #hclust #wgcna #dissimilarity #average
updated 2.4 years ago by ★ 4.0k • written 2.4 years ago by • 0
0
votes
1
reply
827
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 65k • written 2.5 years ago by ▴ 20
0
votes
1
reply
912
views
Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 2.6 years ago by 41k • written 2.6 years ago by • 0
4
votes
1
reply
1.9k
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 2.5 years ago by 41k • written 2.5 years ago by ▴ 10
1
vote
1
reply
780
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 2.2 years ago by 50k • written 2.2 years ago by • 0
2
votes
2
replies
1.4k
views
Need help in determing upregulated and downregulated genes
RNASeqR
3.0 years ago Rishav ▴ 20
0
votes
1
reply
948
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 20 months ago by 41k • written 20 months ago by • 0
1
vote
2
replies
830
views
Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
3
votes
5
replies
2.0k
views
Volcano plot - select additional gene
EnhancedVolcano RNASeqR R volcanoplot
updated 3.5 years ago by ★ 3.9k • written 3.5 years ago by ▴ 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 ▴ 780 • written 3.1 years ago by ▴ 20
0
votes
3
replies
1.3k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 20 months ago by ★ 4.0k • written 20 months ago by • 0
27 results • Page 1 of 1
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Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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