The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.

This is a package for saving GenomicRanges, IRanges and related data structures into file artifacts, and loading them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

ruby-hydra-minimal is a Ruby library for working with hyphenation patterns. It is a low-dependency variant of ruby-hydra.

The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools.

Easily talk to Google's BigQuery Storage API from R (<https://docs.cloud.google.com/bigquery/docs/reference/storage/rpc>).

Extends the BatchJobs package to run statistical experiments on batch computing clusters. For further details see the project web page.

Draws causal hypergraph plots from models output by configurational comparative methods such as Coincidence Analysis (CNA) or Qualitative Comparative Analysis (QCA).

This package provides a set of utilities for manipulating index numbers series including chain-linking, re-referencing, and computing growth rates.

This package provides a function that, as an alternative to base::list, allows default values to be inherited from another list.

Color palettes for data visualization inspired by National Parks. Currently contains 15 color schemes and checks for colorblind-friendliness of palettes.

This contains elisp functions and other useful things for my configuration for Emacs that touches org-roam.

Measuring information flow between time series with Shannon and Rényi transfer entropy. See also Dimpfl and Peter (2013) <doi:10.1515/snde-2012-0044> and Dimpfl and Peter (2014) <doi:10.1016/j.intfin.2014.03.004> for theory and applications to financial time series. Additional references can be found in the theory part of the vignette.

The ratelimiter module ensures that an operation will not be executed more than a given number of times during a given period.

The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data.

Perform competing risks analysis under bivariate Pareto models. See Shih et al. (2019) <doi:10.1080/03610926.2018.1425450> for details.

Extension of testthat package to make unit tests on empirical distributions of estimators and functions for diagnostics of their finite-sample performance.

This package provides functions for the implementation of a density goodness-of-fit test, based on piecewise approximation of the L2 distance.

Random shuffle implementation, on immutable lists. Based on perfect shuffle implementation by Oleg Kiselyov.

Test::Requires checks to see if the module can be loaded. If this fails, then rather than failing tests this skips all tests.

This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages".

The Negative Binomial regression with mean and shape modeling and mean and variance modeling and Beta Binomial regression with mean and dispersion modeling.

Adds menu items to the R Commander for parametric analysis of dichotomous choice contingent valuation (DCCV) data. CV is a question-based survey method to elicit individuals preferences for goods and services. This package depends on functions regarding parametric DCCV analysis in the package DCchoice. See Carson and Hanemann (2005) <doi:10.1016/S1574-0099(05)02017-6> for DCCV.

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.

This minor mode sets background color to strings that match color names, e.g., #0000ff is displayed in white with a blue background.