The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

robot_detection is a python module to detect if a given HTTP User Agent is a web crawler. It uses the list of registered robots from http://www.robotstxt.org.

The binding_of_caller module provides the Binding#of_caller method. It allows accessing bindings from upper frames in the call stack and can evaluate code in that context.

This LaTeX reference sheet is for writing a thesis using the KOMA-Script document classes (scrartcl, scrreprt, scrbook) and all the packages needed for a thesis in natural sciences.

Expands the connector <https://github.com/NovoNordisk-OpenSource/connector> package and provides a convenient interface for accessing and interacting with Databricks <https://www.databricks.com> volumes and tables directly from R.

This module implements an interface to the GNU Readline library. It gives you input line editing facilities, input history management facilities, completion facilities, etc. Term::ReadLine::Gnu is upwards compatible with Term::ReadLine.

emacs-pip-requirements is a major mode for editing pip requirements files, with the following features:

• Syntax highlighting

• Togglable comments

• Auto completion of package names from PyPI

This Emacs package allows you to open a target page on github/gitlab (or bitbucket) by calling browse-at-remote command. It supports dired buffers and opens them in tree mode at destination.

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15.

This package is a visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways.

This Emacs package allows you to open a target page on github/gitlab (or bitbucket) by calling browse-at-remote command. It supports dired buffers and opens them in tree mode at destination.

Provides a simple means of reverse-proxying HTTP requests. The raw approach uses the same technique as leveraged by keter, whereas the WAI approach performs full request/response parsing via WAI and http-conduit.

Can be used to simultaneously estimate networks (Gaussian Graphical Models) in data from different groups or classes via Joint Graphical Lasso. Tuning parameters are selected via information criteria (AIC / BIC / extended BIC) or cross validation.

Prebuilt shiny modules containing tools for viewing data, visualizing data, understanding missing and outlier values within your data and performing simple data analysis. This extends teal framework that supports reproducible research and analysis.

Antitrust analysis of healthcare markets. Contains functions to implement the semiparametric estimation technique described in Raval, Rosenbaum, and Tenn (2017) "A Semiparametric Discrete Choice Model: An Application to Hospital Mergers" <doi:10.1111/ecin.12454>.

This package creates a numeric guide for writing the formula for the determinant of a square matrix (a detguide) as a function of the elements of the matrix and writes out that formula, the symbolic representation.

Aim: Supports the most frequently used methods to combine forecasts. Among others: Simple average, Ordinary Least Squares, Least Absolute Deviation, Constrained Least Squares, Variance-based, Best Individual model, Complete subset regressions and Information-theoretic (information criteria based).

This package aims to simplify working with genomic region / interval data by providing a common interface that lets you access a wide selection of file types and formats for handling genomic region data---all using the same syntax.

This package provides a minor mode for renaming buffers according to project structure. For Python buffers, that will be the whole module name. For temporary files and directories, that will be the relative path from the project root.

This package provides a system for fitting Logistic Curve by Rhodes Method. Method for fitting logistic curve by Rhodes Method is described in A.M.Gun,M.K.Gupta and B.Dasgupta(2019,ISBN:81-87567-81-3).

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.

Support for saving and opening last known pdf position in pdfview mode. Information will be saved relative to the pdf being viewed so ensure pdf-view-restore-filename is in the same directory as the viewing pdf.

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.

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>.