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>.

Last updated 10 days ago

big-databioinformaticsmemory-mapped-fileparallel-computingpolygenic-scorespopulation-structure-inferencesnp-datastatistical-methodsopenblaszlibcppopenmp

11.28 score 200 stars 3 dependents 1.5k scripts 1.4k downloads

bigstatsr - 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>.

Last updated 5 months ago

big-datalarge-matricesmemory-mapped-fileparallel-computingstatistical-methodsopenblascppopenmp

10.39 score 179 stars 16 dependents 394 scripts 2.3k downloads

pcadapt - 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>.

Last updated 5 months ago

cpp

7.76 score 39 stars 327 scripts 756 downloads

bigreadr - 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'.

Last updated 2 years ago

large-datasetread-csvcpp

7.76 score 42 stars 4 dependents 636 scripts 1.8k downloads

bigparallelr - 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.

Last updated 4 months ago

6.34 score 4 stars 19 dependents 76 scripts 2.5k downloads

bigsparser - 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.

Last updated 6 months ago

cpp

5.64 score 10 stars 4 dependents 15 scripts 1.2k downloads

bigutilsr - 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.

Last updated 4 months ago

cpp

5.55 score 10 stars 5 dependents 32 scripts 1.5k downloads

bigassertr - 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.).

Last updated 2 years ago

5.40 score 3 stars 25 dependents 3 scripts 2.2k downloads

rmio - 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>.

Last updated 3 years ago

5.39 score 5 stars 20 dependents 3 scripts 1.6k downloads

runonce - 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.

Last updated 2 years ago

4.51 score 3 stars 4 dependents 18 scripts 707 downloads

mmapcharr - 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.

Last updated 6 years ago

cpp

3.95 score 6 stars 1 dependents 7 scripts 519 downloads

inplace - In-place Operators for R

It provides in-place operators for R that are equivalent to '+=', '-=', '*=', '/=' in C++. Those can be applied on integer|double vectors|matrices. You have also access to sweep operations (in-place).

Last updated 4 years ago

cpp

3.60 score 8 stars 9 scripts 256 downloads

primefactr - Use Prime Factorization for Computations

Use Prime Factorization for simplifying computations, for instance for ratios of large factorials.

Last updated 7 years ago

2.70 score 6 scripts 201 downloads