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rspatial

raster:Geographic Data Analysis and Modeling

Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.

Maintained by Robert J. Hijmans. Last updated 5 days ago.

cpp

163 stars 17.23 score 58k scripts 562 dependents

truecluster

ff:Memory-Efficient Storage of Large Data on Disk and Fast Access Functions

The ff package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section (pagesize) in main memory - the effective virtual memory consumption per ff object. ff supports R's standard atomic data types 'double', 'logical', 'raw' and 'integer' and non-standard atomic types boolean (1 bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned), single (4 byte float with NAs). For example 'quad' allows efficient storage of genomic data as an 'A','T','G','C' factor. The unsigned types support 'circular' arithmetic. There is also support for close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and custom close-to-atomic types. ff not only has native C-support for vectors, matrices and arrays with flexible dimorder (major column-order, major row-order and generalizations for arrays). There is also a ffdf class not unlike data.frames and import/export filters for csv files. ff objects store raw data in binary flat files in native encoding, and complement this with metadata stored in R as physical and virtual attributes. ff objects have well-defined hybrid copying semantics, which gives rise to certain performance improvements through virtualization. ff objects can be stored and reopened across R sessions. ff files can be shared by multiple ff R objects (using different data en/de-coding schemes) in the same process or from multiple R processes to exploit parallelism. A wide choice of finalizer options allows to work with 'permanent' files as well as creating/removing 'temporary' ff files completely transparent to the user. On certain OS/Filesystem combinations, creating the ff files works without notable delay thanks to using sparse file allocation. Several access optimization techniques such as Hybrid Index Preprocessing and Virtualization are implemented to achieve good performance even with large datasets, for example virtual matrix transpose without touching a single byte on disk. Further, to reduce disk I/O, 'logicals' and non-standard data types get stored native and compact on binary flat files i.e. logicals take up exactly 2 bits to represent TRUE, FALSE and NA. Beyond basic access functions, the ff package also provides compatibility functions that facilitate writing code for ff and ram objects and support for batch processing on ff objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely with functionality from package 'bit': chunked looping, fast bit operations and coercions between different objects that can store subscript information ('bit', 'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows to work interactively with selections of large datasets and quickly modify selection criteria. Further high-performance enhancements can be made available upon request.

Maintained by Jens Oehlschlägel. Last updated 3 months ago.

cpp

27 stars 12.01 score 764 scripts 71 dependents

bioc

peakPantheR:Peak Picking and Annotation of High Resolution Experiments

An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.

Maintained by Arnaud Wolfer. Last updated 5 months ago.

massspectrometrymetabolomicspeakdetectionfeature-detectionmass-spectrometry

12 stars 6.65 score 23 scripts

bioc

ReportingTools:Tools for making reports in various formats

The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research-pub.gene.com/ReportingTools.

Maintained by Jason A. Hackney. Last updated 5 months ago.

immunooncologysoftwarevisualizationmicroarrayrnaseqgodatarepresentationgenesetenrichment

6.23 score 93 scripts 1 dependents

r-forge

distrSim:Simulation Classes Based on Package 'distr'

S4-classes for setting up a coherent framework for simulation within the distr family of packages.

Maintained by Peter Ruckdeschel. Last updated 2 months ago.

4.16 score 7 scripts 3 dependents

djhshih

filenamer:Easy Management of File Names

Create descriptive file names with ease. New file names are automatically (but optionally) time stamped and placed in date stamped directories. Streamline your analysis pipeline with input and output file names that have informative tags and proper file extensions.

Maintained by David J. H. Shih. Last updated 12 months ago.

3.92 score 28 scripts 2 dependents

r-forge

distrTEst:Estimation and Testing Classes Based on Package 'distr'

Evaluation (S4-)classes based on package distr for evaluating procedures (estimators/tests) at data/simulation in a unified way.

Maintained by Peter Ruckdeschel. Last updated 2 months ago.

3.68 score 3 scripts 1 dependents

hsonne

pathlist:Package Supporting the Work with File Paths

This package implements a S4 class pathlist that internally stores a vector of file paths (as, e.g. received with dir()) as a matrix of path segments. I found out that this is the most compact form to store the paths. The main feature of the class is the dollar function that allows to filter paths for the value of their top-level folder. Using the dollar operator subsequently you can easily narrow down the list of paths. The class implements functions length(), head(), tail(), summary(), and show().

Maintained by Hauke Sonnenberg. Last updated 6 years ago.

1.78 score 2 scripts 2 dependents

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