Bioconductor Snps

Showing : snps • reset

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3.5k

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snps VCF

updated 3.5 years ago by Arafat • 0 • written 8.7 years ago by rkdonthu ▴ 10

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927

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hierClust R SNPs clustering

updated 3.6 years ago by James W. MacDonald 68k • written 3.6 years ago by sekhwal • 0

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1.4k

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SNPs

6.6 years ago pltbiotech_tkarthi • 0

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1.6k

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snps vcf venn diagram ggplot2

6.9 years ago mictadlo ▴ 10

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1.7k

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bioconductor molecular biology snps

updated 7.0 years ago by James W. MacDonald 68k • written 7.0 years ago by jebreen20 • 0

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3.3k

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motifbreakR vcf snps motif analysis

updated 7.4 years ago by Valerie Obenchain ★ 6.8k • written 7.4 years ago by svlachavas ▴ 840

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2.0k

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

updated 8.4 years ago by Valerie Obenchain ★ 6.8k • written 8.4 years ago by Lna • 0

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1.8k

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hsapiens snps indels

updated 10.0 years ago by Hervé Pagès 16k • written 10.0 years ago by kredens • 0

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2.0k

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Biostrings SNPs alignment

updated 10.3 years ago by Hervé Pagès 16k • written 10.3 years ago by ben.ward ▴ 30

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2.3k

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gviz ideogram snps

updated 10.8 years ago by florian.hahne@novartis.com ★ 1.6k • written 10.8 years ago by vnyirongo • 0

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2.7k

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overlap snps granges iranges

updated 11.1 years ago by Michael Lawrence ★ 11k • written 11.1 years ago by anastasiya-terskih ▴ 10

11 results • Page 1 of 1

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Comment: Getting a large intercept with DESeq2 by Michael Love 43k

Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…

Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k

As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…

Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k

The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …

Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k

There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…

Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k

Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…

Votes

Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif

Using edgeR or DESeq2 to analyze allele-specific expression?

Answer: DESeq2 design for haplotype MPRA

Answer: Failure to download resources (MeSHDb) from AnnotationHub

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