Bioconductor Hg19

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829

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annotation hg19

11 months ago pcantalupo ▴ 10

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2.2k

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genomeinfodb hg19 ucsc seqlevel genomicfeatures

updated 5.1 years ago by James W. MacDonald 68k • written 5.1 years ago by foehn ▴ 100

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1.6k

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hg19 liftover matrixeqtl DMRcate

updated 5.9 years ago by James W. MacDonald 68k • written 5.9 years ago by yoursbassanio ▴ 10

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1.2k

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bsgenome.hsapiens.ucsc.hg19 hg19

updated 7.5 years ago by Mike Smith ★ 6.6k • written 7.5 years ago by addyS • 0

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1.5k

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omiccircos bug hg19 hg18 data

8.0 years ago matthew.bashton • 0

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3.4k

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ucsc ucsctrack ggbio Gviz hg19

updated 8.2 years ago by maximilianh ▴ 10 • written 8.2 years ago by metamaden ▴ 10

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1.5k

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biomart hg19

8.6 years ago Stephane Plaisance | VIB | ▴ 60

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1.4k

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bsgenome hg19

updated 9.6 years ago by Martin Morgan 25k • written 9.6 years ago by Lakshmanan Iyer ▴ 250

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Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k

You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel

Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k

You show how you modified the container, but not how you are running it, which is the critical part.

Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0

Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …

Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k

Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…

Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0

Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…

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Answer: How to combine two DESeq2 objects (dds) for analysis

How to combine two DESeq2 objects (dds) for analysis

How can I correctly use phyloseq with Docker?

A: DESeq2::sizeFactors() function does not output the sizeFactor table.

Comment: Filtering after DESeq

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