Imports: seqinr, igraph, bigmemory, Matrix, foreach, parallel

Imports: seqinr, igraph, bigmemory, Matrix, foreach, parallel, pryr,
Description: Read and preprocess fasta format data, and construct the co-occurrence network for downstream analyses. This R package is to construct the co-occurrence network with the algorithm developed by Du (2008) <DOI:10.1101/gr.6969007>. It could be used to transform the data with high-dimension, such as DNA or protein sequence, into co-occurrence networks. Co-occurrence network could not only capture the co-variation pattern between variables, such as the positions in DNA or protein sequences, but also reflect the relationship between samples. Although it is originally used in DNA and protein sequences, it could be also used to other kinds of data, such as RNA, SNP, etc.

person("Jon", "Harmon", , "jonthegeek@gmail.com", role = c("aut", "cre",
role = c("cph"), comment = "js-cookie JavaScript library"),
role = c("cph"), comment = "js-cookie JavaScript library")
Description: Browser cookies are name-value pairs that are saved in a user's
browser by a website. Cookies allow websites to persist information about
the user and their use of the website. Here we provide tools for working
with cookies in 'shiny' apps, in part by wrapping the 'js-cookie' JavaScript
Suggests: covr, roxygen2, testthat (>= 3.0.0)
Imports: cli, clock, glue, htmltools, httpuv, jsonlite, purrr, rlang,
Author: Jon Harmon [aut, cre, cph] (<https://orcid.org/0000-0003-4781-4346>),
Klaus Hartl [cph] (js-cookie JavaScript library),
Fagner Brack [cph] (js-cookie JavaScript library)

Title: Practical Tools for Scientific Computations and Visualizations
Description: Collection of routines for efficient scientific computations in physics and astrophysics. These routines include utility functions, advanced computation tools, as well as visualisation tools. They can be used, for example, for generating random numbers from spherical and custom distributions, information and entropy analysis, special Fourier transforms, two-point correlation estimation (e.g. as in Landy & Szalay (1993) <doi:10.1086/172900>), binning & gridding of point sets, 2D interpolation, Monte Carlo integration, vector arithmetic and coordinate transformations. Also included is a non-exhaustive list of important constants in astrophysics and cosmological conversion functions. The graphics routines can be used to produce and export publication-ready scientific plots and movies, e.g. as used in Obreschkow et al. (2020) <doi:10.1093/mnras/staa445>. These routines include special color scales, projection functions, and bitmap handling routines.
Imports: magicaxis, plotrix, celestial, data.table, pracma, utils, png,
jpeg, raster, MASS, sp, cubature, bit64, Rcpp