samr v3.0

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SAM: Significance Analysis of Microarrays

Significance Analysis of Microarrays for differential expression analysis, RNAseq data and related problems.

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Web-enabled and Cross-platform SAM via Shiny

This version of SAM provided adds a web interface using Shiny.

Install the current version of the package, after removing any older versions you may have already installed. Later, when this package makes it to CRAN, you will install it the usual way.

The web interface is invoked via:

library(samr)
runSAM()

That will bring up a browser window with a user interface. More details are provided in the manual sam.pdf in this directory

Note that users should use Firefox or Chrome as the _default_browser on Windows: IE will not work.

Michael Seo

Functions in samr

Name Description
runSAM Run the sam webapp
SAM Significance analysis of microarrays - simple user interface
SAMseq Significance analysis of sequencing data - simple user interface
samr.plot Make Q-Q plot for SAM analysis
samr.pvalues.from.perms Report estimated p-values for each gene, from a SAM analysis
samr.estimate.depth estimate the sequencing depth
samr-internal Internal samr functions
samr.missrate Estimate the miss rate table for a SAM analysis
samr.norm.data output normalized sequencing data
samr.compute.delta.table Compute delta table for SAM analysis
samr.compute.siggenes.table Compute significant genes table
samr.tail.strength Estimate tail strength for a dataset, from a SAM analysis
samr.assess.samplesize Assess the sample size for a SAM analysis
samr.assess.samplesize.plot Make a plot of the results from samr.assess.samplesize
samr Significance analysis of microarrays
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Details

biocViews
License LGPL
URL https://statweb.stanford.edu/~tibs/SAM
Packaged 2018-10-16 00:56:47 UTC; tibs
Repository CRAN
Date/Publication 2018-10-16 10:00:03 UTC
NeedsCompilation yes

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