Bioconductor Sigcheck

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SigCheck

updated 5.7 years ago by Rory Stark ★ 5.2k • written 5.7 years ago by Lavorgna Giovanni ▴ 80

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SigCheck sigcheck

8.9 years ago Rory Stark ★ 5.2k

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Answer: Allele frequencies for ALL alleles of one SNP ? by Abiologist • 0

I've discovered that rsnps::ncbi_snp_query(snp_id) does actually give this information - at the bottom of the result$maf_population table. …

Answer: Identifying potentially associated gene set to drug response using GSVA by Robert Castelo ★ 3.4k

Hi, if you want to do some formal inference about the effect of a drug at RNA level, then I would recommend you doing a differential expres…

Answer: How to get The evolutionary conservation scores for lncRNAs by the phastCons100w by Robert Castelo ★ 3.4k

The `phastCons100way.UCSC.hg38` annotation package, storing conservation scores of the human genome version `hg38`, should be queried with …

Comment: Package needs internet access by firestar ▴ 20

That worked! Thanks! I created the genome file locally and uploaded that. I didn't really think that BSgenome.Hsapiens.UCSC.hg38 was only u…

Comment: limma technical repeat correction by john • 0

Hi @gordonsmyth, Thank you very much for your response. The normalization process involves multiple steps and they provide a normalised f…

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Answer: Package needs internet access

Dotplot from enricher outputting very few genes

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