X - Certificate and Key management
This application is intended for creating and managing X.509
certificates, certificate requests, RSA, DSA and EC private keys,
Smartcards and CRLs. Everything that is needed for a CA is
implemented. All CAs can sign sub-CAs recursively. These certificate
chains are shown clearly. For an easy company-wide use there are
customiseable templates that can be used for certificate or request
generation.
All cryptographic data is stored in a SQL database. SQLite, MySQL
(MariaDB) and PostgreSQL databases are supported.
The package is a development of nfssext.sty, distributed with
the examples for the font installation guide. The package has
been developed for use in packages such as cfr-lm and
venturisadf.
The package enables the user to use beamer style operations on
a canvas of the sizes provided by a0poster; font scaling is
available (using packages such as type1cm if necessary). In
addition, the package allows the user to benefit from the nice
colour box handling and alignment provided by the beamer class
(for example, with rounded corners and shadows). Good looking
posters may be created very rapidly. Features include: scalable
fonts using the fp and type1cm packages; posters in A-series
sizes, and custom sizes like double A0 are possible; still
applicable to custom beamer slides, e.g. 16:9 slides for a
wide-screen (i.e. 1.78 aspect ratio); orientation may be
portrait or landscape; a 'debug mode' is provided.
The package provides the command \chemfig{<code>}, which draws
molecules using the TikZ package. The <code> argument provides
instructions for the drawing operation. While the diagrams
produced are essentially 2-dimensional, the package supports
many of the conventional notations for illustrating the
3-dimensional layout of a molecule. The package uses TikZ for
its actual drawing operations.
The Biopython package contains high-quality, reusable modules and
scripts written in Python to make it as easy as possible to use Python
for bioinformatics. The Biopython includes the follwing: the ability
to parse bioinformatics files into python utilizable data structures,
including support for the formats such as Blast output, Clustalw,
FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP,
Rebase, UniGene, and SwissProt.
Collection of functions and layers to enhance 'ggplot2'. The flagship
function is 'ggMarginal()', which can be used to add marginal
histograms/boxplots/density plots to 'ggplot2' scatterplots.
A colour picker that can be used as an input in Shiny apps or
Rmarkdown documents. The colour picker supports alpha opacity, custom
colour palettes, and many more options. A Plot Colour Helper tool is
available as an RStudio Addin, which helps you pick colours to use in
your plots. A more generic Colour Picker RStudio Addin is also
provided to let you select colours to use in your R code.
Perform common useful JavaScript operations in Shiny apps that will
greatly improve your apps without having to know any JavaScript.
Examples include: hiding an element, disabling an input, resetting an
input back to its original value, delaying code execution by a few
seconds, and many more useful functions for both the end user and the
developer. 'shinyjs' can also be used to easily call your own custom
JavaScript functions from R.
Makes it incredibly easy to build interactive web applications with R.
Automatic "reactive" binding between inputs and outputs and extensive
prebuilt widgets make it possible to build beautiful, responsive, and
powerful applications with minimal effort.
Provides low-level socket and protocol support for handling HTTP and
WebSocket requests directly from within R. It is primarily intended as
a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv
alone. httpuv is built on top of the libuv and http-parser C
libraries, both of which were developed by Joyent, Inc. (See LICENSE
file for libuv and http-parser license information.)
Provides fundamental abstractions for doing asynchronous programming
in R using promises. Asynchronous programming is useful for allowing a
single R process to orchestrate multiple tasks in the background while
also attending to something else. Semantics are similar to
'JavaScript' promises, but with a syntax that is idiomatic R.
Generate your Rd documentation, 'NAMESPACE' file, and collation field
using specially formatted comments. Writing documentation in-line with
code makes it easier to keep your documentation up-to-date as your
requirements change. 'Roxygen2' is inspired by the 'Doxygen' system
for C++.
Simulates the process of installing a package and then attaching it.
This is a key part of the 'devtools' package as it allows you to
rapidly iterate while developing a package.
Run 'R CMD check' from 'R' and capture the results of the individual
checks. Supports running checks in the background, timeouts, pretty
printing and comparing check results.
Automate package and project setup tasks that are otherwise performed
manually. This includes setting up unit testing, test coverage,
continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio'
projects, and more.
Useful tools for working with HTTP organised by HTTP verbs (GET(),
POST(), etc). Configuration functions make it easy to control
additional request components (authenticate(), add_headers() and so
on).
Provides functions used to build R packages. Locates compilers needed
to build R packages on various platforms and ensures the PATH is
configured appropriately so R can use them.
It is sometimes useful to perform a computation in a separate R
process, without affecting the current R process at all. This packages
does exactly that.
Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519.
Cryptographic signatures can either be created and verified manually
or via x509 certificates. AES can be used in cbc, ctr or gcm mode for
symmetric encryption; RSA for asymmetric (public key) encryption or EC
for Diffie Hellman. High-level envelope functions combine RSA and AES
for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a
secure random number generator, and 'bignum' math methods for manually
performing crypto calculations on large multibyte integers.
Tools to run system processes in the background. It can check if a
background process is running; wait on a background process to finish;
get the exit status of finished processes; kill background processes.
It can read the standard output and error of the processes, using
non-blocking connections. 'processx' can poll a process for standard
output or error, with a timeout. It can also poll several processes at
once.
Cross-platform utilities for prompting the user for credentials or a
passphrase, for example to authenticate with a server or read a
protected key. Includes native programs for MacOS and Windows, hence
no 'tcltk' is required. Password entry can be invoked in two different
ways: directly from R via the askpass() function, or indirectly as
password-entry back-end for 'ssh-agent' or 'git-credential' via the
SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user
can be prompted for credentials or a passphrase if needed when R calls
out to git or ssh.
Software testing is important, but, in part because it is frustrating
and boring, many of us avoid it. 'testthat' is a testing framework for
R that is easy to learn and use, and integrates with your existing
'workflow'.
Interface to the 'libgit2' library, which is a pure C implementation
of the 'Git' core methods. Provides access to 'Git' repositories to
extract data and running some basic 'Git' commands.
Drop-in replacements for the base system2() function with fine control
and consistent behavior across platforms. Supports clean interruption,
timeout, background tasks, and streaming STDIN / STDOUT / STDERR over
binary or text connections. Arguments on Windows automatically get
encoded and quoted to work on different locales.
Robust, reliable and flexible paths to files below a project root. The
'root' of a project is defined as a directory that matches a certain
criterion, e.g., it contains a certain regular file.
Query and print information about the current R session. It is similar
to 'utils::sessionInfo()', but includes more information about
packages, and where they were installed from.
Download and install R packages stored in 'GitHub', 'BitBucket', or
plain 'subversion' or 'git' repositories. This package provides the
'install_*' functions in 'devtools'. Indeed most of the code was
copied over from 'devtools'.
brew implements a templating framework for mixing text and R code for
report generation. brew template syntax is similar to PHP, Ruby's erb
module, Java Server Pages, and Python's psp module.
The CommonMark specification defines a rationalized version of
markdown syntax. This package uses the 'cmark' reference
implementation for converting markdown text into various formats
including html, latex and groff man. In addition it exposes the
markdown parse tree in xml format. Also includes opt-in support for
GFM extensions including tables, autolinks, and strikethrough text.
A small subset of Unicode symbols, that are useful when building
command line applications. They fall back to alternatives on terminals
that do not support Unicode. Many symbols were taken from the
'figures' 'npm' package (see
<https://github.com/sindresorhus/figures>).
Parse simple '.ini' configuration files to an structured list. Users
can manipulate this resulting list with lapply() functions. This same
structured list can be used to write back to file after modifications.
An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
A backend for the selecting functions of the 'tidyverse'. It makes it
easy to implement select-like functions in your own packages in a way
that is consistent with other 'tidyverse' interfaces for selection.
Extends the functionality of 'ggplot2', providing the capability to
plot ternary diagrams for (subset of) the 'ggplot2' geometries.
Additionally, 'ggtern' has implemented several NEW geometries which
are unavailable to the standard 'ggplot2' release. For further
examples and documentation, please proceed to the 'ggtern' website.
Provides functions for the consistent analysis of compositional data
(e.g. portions of substances) and positive numbers (e.g.
concentrations) in the way proposed by J. Aitchison and V.
Pawlowsky-Glahn.
"Essential" Robust Statistics. Tools allowing to analyze data with
robust methods. This includes regression methodology including model
selections and multivariate statistics where we strive to cover the
book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and
Yohai'; Wiley 2006.
