Bioconductor SNPs

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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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912

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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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1.3k

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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

6.8 years ago mictadlo ▴ 10

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1.7k

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bioconductor molecular biology snps

updated 6.9 years ago by James W. MacDonald 68k • written 6.9 years ago by jebreen20 • 0

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3.2k

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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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1.9k

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

updated 8.3 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 9.9 years ago by Hervé Pagès 16k • written 9.9 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: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k

Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…

Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20

thank you so much for answering Dr. Love!

Answer: DESeq2 for candidate gene analysis by Michael Love 43k

Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k

Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…

Votes

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

Answer: DESeq2 for candidate gene analysis

DESeq2 for candidate gene analysis

Answer: DESeq2 for candidate gene analysis

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