Artifacts using Digest (171)

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For natural language processing and analysis of qualitative text coding structures which provide a way to bind together text and text data are fundamental. The package provides such a structure and accompanying methods in form of R6 objects. The 'rtext' class allows for text handling and text coding (character or regex based) including data updates on text transformations as well as aggregation on various levels. Furthermore, the usage of R6 enables inheritance and passing by reference which should enable ...

Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.

Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive features : panning, zooming, tooltips, etc.

A 'ggplot2' extension to visualize two variables through one color aesthetic via mapping to a color space projection. With this technique for 2-D color mapping, one can create a bivariate choropleth in R as well as other visualizations with multivariate color scales. Includes two new scales and a new guide for 'ggplot2'.

annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl.

The package provides functionality to extract isotopic peak patterns from raw mass spectra. This is done by fitting a large set of template basis functions to the raw spectrum using either nonnegative least squares or least absolute deviation fittting. The package offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the data. The package also provides functionality to process LCMS runs.

Memory-efficient reading, writing, and manipulation of structured binary data on disk as vectors, matrices, arrays, lists, and data frames.

PanViz is a JavaScript based visualisation tool for functionaly annotated pangenomes. PanVizGenerator is a companion for PanViz that facilitates the necessary data preprocessing step necessary to create a working PanViz visualization. The output is fully self-contained so the recipient of the visualization does not need R or PanVizGenerator installed.

A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes ...

Generator of web pages which display interactive network/graph visualizations with D3js, jQuery and Raphael.