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r-geo2rnaseq
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public |
RNA-seq is a method that uses next-generation sequencing to quantify and analyze RNA. It can be used for finding significantly differentially expressed genes (DEGs) in well sequenced organisms. This package is a complete function library for analyzing read files, trimming of raw reads, mapping on reference genomes, counting reads per gene and finding significant DEGs.
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2023-06-16 |
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r-protoclust
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public |
Performs minimax linkage hierarchical clustering. Every cluster has an associated prototype element that represents that cluster as described in Bien, J., and Tibshirani, R. (2011), "Hierarchical Clustering with Prototypes via Minimax Linkage," accepted for publication in The Journal of the American Statistical Association, DOI: 10.1198/jasa.2011.tm10183.
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2023-06-16 |
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r-poissonseq
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public |
This package implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data. The description of the method is in Li J, Witten DM, Johnstone I, Tibshirani R (2012). Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics 13(3): 523-38. We estimate the sequencing depths of experiments using a new method based on Poisson goodness-of-fit statistic, calculate a score statistic on the basis of a Poisson log-linear model, and then estimate the false discovery rate using a modified version of permutation plug-in method. A more detailed instruction as well as sample data is available at http://www.stanford.edu/~junli07/research.html. In this version, we changed the way of calculating log foldchange for two-class data. The FDR estimation part remains unchanged.
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2023-06-16 |
