Using GPUs in Statistical Genomics

Can be used to carry out permutation resampling inference in the context of RNA microarray studies.


permGPU changes

changes in permGPU 0.14.8

  • minor fixes

changes in permGPU 0.14.7

  • fixed out of date syntax in Makefile

  • minor fixes

changes in permGPU 0.14.6

  • added dependency on "survival" package

  • improved test calculation result checks

changes in permGPU 0.14.5

  • test calculation result checks are added

changes in permGPU 0.14.4

  • fixing note related to importing dependent packages

changes in permGPU 0.14.3

  • fixing bugs and clearing code

changes in permGPU 0.14.2

  • fixes to scoregpu and permgpu when little or no variability in expression

changes in permGPU 0.14.1

  • scoregpu incorporates permutation

changes in permGPU 0.14

  • Functions for computing Cox (rank) score test statistic

changes in permGPU 0.13

  • Cox test statistic is faster for data sets with large number of events

  • Cox test handles missing data

changes in permGPU 0.12

  • permGPU uses the R random number generator

changes in permGPU 0.11

  • Cox rank score test statistic is added

  • Pearson, Spearman and Cox test statistics are standardized

Reference manual

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0.15 by Ivo D. Shterev, 8 months ago

Browse source code at

Authors: Ivo D. Shterev [aut, cre] , Kouros Owzar [aut] , Sin-Ho Jung [aut] , Stephen L. George [aut] , Brian J. Smith [ctb, cph] (wrote original version of file) , Kenneth Wilder [ctb, cph] (wrote ranker.h) , Romain Francois [ctb, cph] (wrote original version of cleanup file) , Dirk Eddelbuettel [ctb, cph] (wrote original version of cleanup file)

Documentation:   PDF Manual  

Task views: High-Performance and Parallel Computing with R

GPL-3 license

Depends on Biobase, RUnit, foreach, survival, methods

System requirements: Nvidia's CUDA toolkit (>= release 6.0)

See at CRAN