Bioconductor SNPs

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3.0k

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snps VCF

updated 2.6 years ago by Arafat • 0 • written 7.8 years ago by rkdonthu ▴ 10

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740

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hierClust R SNPs clustering

updated 2.7 years ago by James W. MacDonald 67k • written 2.7 years ago by sekhwal • 0

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1.1k

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SNPs

5.7 years ago pltbiotech_tkarthi • 0

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1.4k

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snps vcf venn diagram ggplot2

5.9 years ago mictadlo ▴ 10

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1.4k

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bioconductor molecular biology snps

updated 6.0 years ago by James W. MacDonald 67k • written 6.0 years ago by jebreen20 • 0

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2.8k

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motifbreakR vcf snps motif analysis

updated 6.4 years ago by Valerie Obenchain ★ 6.8k • written 6.4 years ago by svlachavas ▴ 840

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1.6k

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variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc

updated 7.4 years ago by Valerie Obenchain ★ 6.8k • written 7.4 years ago by Lna • 0

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1.6k

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hsapiens snps indels

updated 9.0 years ago by Hervé Pagès 16k • written 9.0 years ago by kredens • 0

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1.7k

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Biostrings SNPs alignment

updated 9.3 years ago by Hervé Pagès 16k • written 9.4 years ago by ben.ward ▴ 30

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2.0k

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gviz ideogram snps

updated 9.8 years ago by florian.hahne@novartis.com ★ 1.6k • written 9.8 years ago by vnyirongo • 0

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2.4k

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overlap snps granges iranges

updated 10.1 years ago by Michael Lawrence ★ 11k • written 10.1 years ago by anastasiya-terskih ▴ 10

11 results • Page 1 of 1

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Answer: Epic v2 Annotation CpG_maf source? by James W. MacDonald 67k

Those all come from dbSNP by way of UCSC. [See here][1], particularly lines 114 and onward. Here is no MAF for a CpG. The MAF is for the…

Comment: Deseq2 res Function by James W. MacDonald 67k

In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your co…

Answer: Struggle with the replicates of epic array data by James W. MacDonald 67k

You shouldn't be using beta values for a linear model that assumes a unimodal, untruncated distribution (beta values are strictly on (0-1) …

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

So, if I understand correctly, you derived GSVA scores from gene sets corresponding somehow to drugs in your RNA-seq data. Since GSVA score…

Answer: Deseq2 res Function by Michael Love 43k

> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…

Votes

Appropriate use of the function treat of the limma package

Comment: Is it recommended to analyze different tissues together when using edgeR

Answer: Deseq2 res Function

Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification

Answer: ANOVA like approach of edgeR

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