Bioconductor Geneoverlap

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GeneOverlap heatmaps

10 months ago Johanna • 0

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GeneOverlap multiple figures heatmap

updated 5.2 years ago by James W. MacDonald 68k • written 5.2 years ago by C T ▴ 140

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genomicranges geneoverlap findoverlaps

updated 9.0 years ago by Michael Lawrence ★ 11k • written 9.0 years ago by yao.h.1988 • 0

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GeneOverlap DEGgenes affymetrixchip bioconductor

10.0 years ago svlachavas ▴ 840

4 results • Page 1 of 1

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Answer: fast apply on RleList by story.benjamin ▴ 20

solved with viewApply (code is simplified below) + map reduce on chrs test.split <- split(test.gr,seqnames(test.gr)) final.st…

Comment: fast apply on RleList by story.benjamin ▴ 20

Hi James, thanks for the reply. I ultimately figured it out ... viewApply showed a massive speed increase for me (see other answer) - I was…

Answer: fast apply on RleList by James W. MacDonald 68k

There is already a 'mean' function that will dispatch on an `RleList` that you can use. I don't have a long `RleList` in hand to test it on…

Answer: Custom CDF creation for HTA 2.0 array using GTF annotation by James W. MacDonald 68k

It doesn't appear that Manhong Dai is working at UM any longer, and the webpage appears to have fallen into disrepair (for example, the lin…

Comment: how to use `arrayWeightsQuick()`? by matthew • 0

In the specific use-case I have in mind, `expression` is a simple `matrix` of log2 gene expression per sample, no missing values.

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Answer: fast apply on RleList

Answer: BiocParallel_1.40.1.tar.gz not available

Modelling gene program dynamics across time with {lemur}

A: DESeq2 one group vs multiple groups comparison in presence of batch effect

Comment: BiocParallel_1.40.1.tar.gz not available

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