Showing : RNA Seq • reset
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How to create manhattan plot with DESeq2
deseq2 mahattan plot RNA Seq
updated 22 months ago by ▴ 140 • written 2.8 years ago by • 0
2
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5
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1.3k
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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 13k • written 2.3 years ago by ▴ 800
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3
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287
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Normalization of RNA seq data
RNA seq cpm
updated 2.3 years ago by 3.6k • written 2.3 years ago by • 0
3
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3
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378
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Custom gene annotations for SGSeq
sgseq alternative splicing rna seq
updated 2.7 years ago by ▴ 110 • written 2.7 years ago by • 0
1
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4
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354
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Difference between Fold Changes from EdgeR glmLRTest and directly calculated fold changes.
edger RNA Seq
updated 2.7 years ago by 60k • written 2.7 years ago by ▴ 30
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searching for specific RNA sequences
rna seq
2.7 years ago adeler001 • 0
0
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2
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353
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using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq SGSeq Alternative splicing
updated 2.8 years ago by ▴ 110 • written 2.8 years ago by • 0
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1
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51 views DESeq2 RNAseq differential expression analysis
deseq2 likelihood ratio rna seq wald test
updated 2.9 years ago by 37k • written 2.9 years ago by • 0
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2
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467
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Need help cprrecting overlappinge genes on valcano plot
volcano plot rna seq
updated 3.0 years ago by 37k • written 3.0 years ago by • 0
1
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5
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604
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Time course experiment using limma with voom
limma voom RNA Seq Time-course experiments
updated 3.2 years ago by ★ 27k • written 3.2 years ago by • 0
5
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3
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Steep dendrograms and few modules. WGCNA on RNA seq data
RNA seq wgcna
updated 3.2 years ago by ★ 2.7k • written 3.2 years ago by ▴ 10
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2
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adapter trimming paired vs unpaired reads
rna seq trimmomatic trimming adapter trimming paired analysis
3.3 years ago Mozart ▴ 20
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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
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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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