Bioconductor MethylationArrayData

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MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData

6 weeks ago • updated 4 weeks ago Giovanni Calice ▴ 160

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Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm

4 months ago kyj2226 • 0

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MethylationArrayData methylationArrayAnalysis

5 months ago aldea85 • 0

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MethylationArrayData methylationArrayAnalysis

updated 8 months ago by James W. MacDonald 65k • written 8 months ago by hayleyw • 0

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GeneExpression Bioconductor GEOquery MethylationArrayData

9 months ago Arianna • 0

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MethylationArrayData methylationArrayAnalysis

10 months ago Irene • 0

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methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray

updated 11 months ago by belinda.phipson ▴ 40 • written 11 months ago by Grace • 0

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DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray

updated 11 months ago by Tim Peters ▴ 170 • written 11 months ago by Grace • 0

8 results • Page 1 of 1

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Answer: OrgDb for maize by James W. MacDonald 65k

``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…

Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0

Understood, Thank you very much for the reply, very kind.

Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k

"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…

Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k

These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…

Comment: DEG with low counts by Michael Love 41k

These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…

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Install/Switch between multiple versions of R, Rstudio, and Bioconductor

A: Docker container with bioconductor and devtools

Answer: OrgDb for maize

Comment: significant difference of p-values with dream() after updating VariancePartition

How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

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