bigsnpr - Analysis of Massive SNP Arrays
Easy-to-use, efficient, flexible and scalable tools for analyzing massive SNP arrays. Privé et al. (2018) <doi:10.1093/bioinformatics/bty185>.
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big-databioinformaticsmemory-mapped-fileparallel-computingpolygenic-scorespopulation-structure-inferencesnp-datastatistical-methodsopenblaszlibcppopenmp
11.60 score 220 stars 10 dependents 1.7k scripts 2.0k downloadsbigstatsr - Statistical Tools for Filebacked Big Matrices
Easy-to-use, efficient, flexible and scalable statistical tools. Package bigstatsr provides and uses Filebacked Big Matrices via memory-mapping. It provides for instance matrix operations, Principal Component Analysis, sparse linear supervised models, utility functions and more <doi:10.1093/bioinformatics/bty185>.
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big-datalarge-matricesmemory-mapped-fileparallel-computingstatistical-methodsopenblascppopenmp
11.57 score 180 stars 43 dependents 499 scripts 7.6k downloadsbigreadr - Read Large Text Files
Read large text files by splitting them in smaller files. Package 'bigreadr' also provides some convenient wrappers around fread() and fwrite() from package 'data.table'.
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large-datasetread-csvcpp
8.70 score 43 stars 11 dependents 649 scripts 5.5k downloadspcadapt - Fast Principal Component Analysis for Outlier Detection
Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis. Implements the method described in (Luu, 2016) <DOI:10.1111/1755-0998.12592> and later revised in (Privé, 2020) <DOI:10.1093/molbev/msaa053>.
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cpp
7.45 score 45 stars 422 scripts 762 downloadsbigparallelr - Easy Parallel Tools
Utility functions for easy parallelism in R. Include some reexports from other packages, utility functions for splitting and parallelizing over blocks, and choosing and setting the number of cores used.
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7.36 score 5 stars 46 dependents 81 scripts 8.3k downloadsbigutilsr - Utility Functions for Large-scale Data
Utility functions for large-scale data. For now, package 'bigutilsr' mainly includes functions for outlier detection and unbiased PCA projection.
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cpp
6.86 score 12 stars 12 dependents 45 scripts 7.5k downloadsbigassertr - Assertion and Message Functions
Enhanced message functions (cat() / message() / warning() / error()) using wrappers around sprintf(). Also, multiple assertion functions (e.g. to check class, length, values, files, arguments, etc.).
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6.76 score 4 stars 52 dependents 10 scripts 9.2k downloadsrmio - Provides 'mio' C++11 Header Files
Provides header files of 'mio', a cross-platform C++11 header-only library for memory mapped file IO <https://github.com/mandreyel/mio>.
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6.36 score 5 stars 47 dependents 4 scripts 6.6k downloadsbigsparser - Sparse Matrix Format with Data on Disk
Provide a sparse matrix format with data stored on disk, to be used in both R and C++. This is intended for more efficient use of sparse data in C++ and also when parallelizing, since data on disk does not need copying. Only a limited number of features will be implemented. For now, conversion can be performed from a 'dgCMatrix' or a 'dsCMatrix' from R package 'Matrix'. A new compact format is also now available.
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cpp
5.72 score 10 stars 11 dependents 18 scripts 1.8k downloadsrunonce - Run Once and Save Result
Package 'runonce' helps automating the saving of long-running code to help running the same code multiple times. If you run some long-running code once, it saves the result in a file on disk. Then, if the result already exists, i.e. if the code has already been run and its output has already been saved, it just reads the result from the stored file instead of running the code again.
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5.68 score 4 stars 11 dependents 21 scripts 1.7k downloadsmmapcharr - Memory-Map Character Files
Uses memory-mapping to enable the random access of elements of a text file of characters separated by characters as if it were a simple R(cpp) matrix.
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cpp
3.88 score 5 stars 1 dependents 8 scripts 693 downloadsprimefactr - Use Prime Factorization for Computations
Use Prime Factorization for simplifying computations, for instance for ratios of large factorials.
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2.70 score 9 scripts 175 downloads