Bioconductor Permutation

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modulePreservation WGCNA modules significance permutation

7.5 years ago • updated 5.6 years ago harelarik ▴ 60

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777

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permutation randomization

5.6 years ago Bogdan ▴ 670

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1.5k

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permutation pool chippeakanno

7.2 years ago ge2sasag • 0

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illumina plink permutation

updated 9.4 years ago by James W. MacDonald 68k • written 9.4 years ago by sedrinne • 0

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deseq2 limma edger permutation

updated 22 months ago by Gordon Smyth 53k • written 9.6 years ago by Radek ▴ 90

5 results • Page 1 of 1

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Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0

Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…

Comment: DESeq2 design for haplotype MPRA by Rita • 0

Thank you very much, I appreciate it!

Answer: DESeq2 design for haplotype MPRA by Michael Love 43k

> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…

Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k

It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…

Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k

R-4.5.1 is compatible with both release and devel versions of Bioconductor. Which one are you using? I am still on release, and it's fine: …

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Comment: Check removeBatchEffect effectiveness

Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?

Answer: DESeq2 design for haplotype MPRA

A: Different logFC (log2foldchange) values for genes from limma-voom and other too

Comment: Check removeBatchEffect effectiveness

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