This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

Includes the 100 datasets simulated by Congreve and Lamsdell (2016) <doi:10.1111/pala.12236>, and analyses of the partition and quartet distance of reconstructed trees from the generative tree, as analysed by Smith (2019) <doi:10.1098/rsbl.2018.0632>.

This package provides a tm Source to create corpora from articles exported from the Europresse content provider as HTML files. It is able to read both text content and meta-data information (including source, date, title, author and pages).

Calculates the T-Statistic for the drift burst hypothesis from the working paper Christensen, Oomen and Reno (2018) <DOI:10.2139/ssrn.2842535>. The authors MATLAB code is available upon request, see: <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=2842535>.

This package defines an S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.

This package provides a set of predicates and assertions for checking the properties of variables, such as length, names and attributes. This is mainly for use by other package developers who want to include run-time testing features in their own packages.

If the std or alloc features are enabled, this crate provides implementations for Box, Vec, BTreeMap, and BTreeSet. If the std feature is enabled, this crate additionally provides implementations for HashMap and HashSet.

If the std or alloc features are enabled, this crate provides implementations for Box, Vec, BTreeMap, and BTreeSet. If the std feature is enabled, this crate additionally provides implementations for HashMap and HashSet.

Measures the degree of balance for a given phylogenetic tree by calculating the Total Cophenetic Index. Reference: A. Mir, F. Rossello, L. A. Rotger (2013). A new balance index for phylogenetic trees. Math. Biosci. 241, 125-136 <doi:10.1016/j.mbs.2012.10.005>.

Did you ever feel that C-y M-y M-y M-y ... is not a great way of trying to find that piece of text you know you killed a while back? Then browse-kill-ring.el is for you.

Series of algorithms to translate users mental models of seascapes, landscapes and, more generally, of geographic features into computer representations (classifications). Spaces and geographic objects are classified with user-defined rules taking into account spatial data as well as spatial relationships among different classes and objects.

This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects.

Users can build a single shiny app for exploring population characterization, population-level causal effect estimation, and patient-level prediction results generated via the R analyses packages in HADES (see <https://ohdsi.github.io/Hades/>). Learn more about OhdsiShinyAppBuilder at <https://ohdsi.github.io/OhdsiShinyAppBuilder/>.

MultiAssayExperiment harmonizes data management of multiple assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames.

Extract results into R from the Observational Health Data Sciences and Informatics result database (see <https://ohdsi.github.io/Strategus/results-schema/index.html>) and generate reports/presentations via quarto that summarize results in HTML format. Learn more about OhdsiReportGenerator at <https://ohdsi.github.io/OhdsiReportGenerator/>.

Package regexp implements regular expression search. The syntax of the regular expressions accepted is the same general syntax used by Perl, Python, and other languages. More precisely, it is the syntax accepted by RE2 and described at https://golang.org/s/re2syntax, except for \C.

Analytical power calculations for GxE and GxG interactions for case-control studies of candidate genes and genome-wide association studies (GWAS). This includes power calculation for four two-step screening and testing procedures. It can also calculate power for GxE and GxG without any screening.

The gap statistic approach is extended to estimate the number of clusters for categorical response format data. This approach and accompanying software is designed to be used with the output of any clustering algorithm and with distances specifically designed for categorical (i.e. multiple choice) or ordinal survey response data.

Run Paris Agreement Capital Transition Assessment ('PACTA') analyses on multiple loan books in a structured way. Provides access to standard PACTA metrics and additional PACTA'-related metrics for multiple loan books. Results take the form of csv files and plots and are exported to user-specified project paths.

Package with multivariate analysis methodologies for experiment evaluation. The package estimates dissimilarity measures, builds dendrograms, obtains MANOVA, principal components, canonical variables, etc. (Pacote com metodologias de analise multivariada para avaliação de experimentos. O pacote estima medidas de dissimilaridade, construi de dendogramas, obtem a MANOVA, componentes principais, variaveis canonicas, etc.).

This library enables path variables in networking routes when using Hunchenissr for Common Lisp. If a part of the path (between two slashes) starts with a question mark (?), that symbol (without question mark) will be bound to whatever value was in the same place in the URL (as a string).

This module is for reading record-oriented data in a delimited text file. The most common example have records separated by newlines and fields separated by commas or tabs, but this module aims to provide a consistent interface for handling sequential records in a file however they may be delimited.

This package provides a candidate correspondence table between two classifications can be created when there are correspondence tables leading from the first classification to the second one via intermediate pivot classifications. The correspondence table between two statistical classifications can be updated when one of the classifications gets updated to a new version.

This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580).