Chromosome files in the Fasta format usually contain large sequences like human genome. Sometimes users have to split these chromosomes into different files according to their chromosome number. The chromseq can help to handle this. So the selected chromosome sequence can be used for downstream analysis like motif finding. Howard Y. Chang(2019) <doi:10.1038/s41587-019-0206-z>.
Hospital data analysis workflow tools, modeling, and automations. This library provides many useful tools to review common administrative hospital data. Some of these include average length of stay, readmission rates, average net pay amounts by service lines just to name a few. The aim is to provide a simple and consistent verb framework that takes the guesswork out of everything.
This package provides features that allow users to download weather data published by the Japan Meteorological Agency (JMA) website (<https://www.jma.go.jp/jma/index.html>). The data includes information dating back to 1976 and aligns with the categories available on the website. Additionally, users can process the best track data of typhoons and easily handle earthquake record files.
Stability based methods for model order selection in clustering problems (Valentini, G (2007), <doi:10.1093/bioinformatics/btl600>). Using multiple perturbations of the data the stability of clustering solutions is assessed. Different perturbations may be used: resampling techniques, random projections and noise injection. Stability measures for the estimate of clustering solutions and statistical tests to assess their significance are provided.
Calculate various functions needed for design and monitoring clinical trials with negative binomial endpoint with variable follow-up. This version has a few changes compared to the previous version 1.0.0, including (1) correct a typo in Type 1 censoring, mtbnull=bnull and (2) restructure the code to account for shape parameter equal to zero, i.e. Poisson scenario.
Distance based bipartite matching using minimum cost flow, oriented to matching of treatment and control groups in observational studies ('Hansen and Klopfer 2006 <doi:10.1198/106186006X137047>). Routines are provided to generate distances from generalised linear models (propensity score matching), formulas giving variables on which to limit matched distances, stratified or exact matching directives, or calipers, alone or in combination.
Analysis of features by phi delta diagrams. In particular, functions for reading data and calculating phi and delta as well as the functionality to plot it. Moreover it is possible to do further analysis on the data by generating rankings. For more information on phi delta diagrams, see also Giuliano Armano (2015) <doi:10.1016/j.ins.2015.07.028>.
Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the STACOMI open source project developed in France by the French Office for Biodiversity institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on STACOMI'.
Simulates data sets in order to explore modeling techniques or better understand data generating processes. The user specifies a set of relationships between covariates, and generates data based on these specifications. The final data sets can represent data from randomized control trials, repeated measure (longitudinal) designs, and cluster randomized trials. Missingness can be generated using various mechanisms (MCAR, MAR, NMAR).
This package provides a collection of useful functions and example code created and used by the Schloss Lab for reproducible microbiome research. Perform common tasks like read files created by mothur <https://mothur.org/>, tidy up your microbiome data, and format R Markdown documents for publication. See the website <http://www.schlosslab.org/schtools/> for more information, documentation, and examples.
Srt file is a common subtitle format for videos, it contains subtitle and when the subtitle showed. This package is for align time of srt file, and also change color, style and position of subtitle in videos, the srt file will be read as a vector into R, and can be write into srt file after modified using this package.
This package provides a shiny interface for a simpler use of the sbm R package. It also contains useful functions to easily explore the sbm package results. With this package you should be able to use the stochastic block model without any knowledge in R, get automatic reports and nice visuals, as well as learning the basic functions of sbm'.
Graphical tools for visualizing high-dimensional data along a path of alternating one- and two-dimensional plots. Note that this includes interactive graphics plots based on loon in turn based on tcltk (included as part of the standard R distribution). It also requires graph from Bioconductor. For more detail on use and algorithms, see <doi:10.18637/jss.v095.i04>.
Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data could be used as an example supporting BloodGen3Module R package.
RaySession is a session manager for audio programs such as Ardour, Carla, QTractor, Guitarix, Patroneo, Jack Mixer, etc. The principle is to load together audio programs, then be able to save or close all documents together. Its main purpose is to manage NSM compatible programs, but it also helps for other programs. It offers a patchbay for visualizing and editing connections.
The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as Latent Dirichlet Allocation (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single cell epigenomics data, and includes functionalities to identify cell states based on the contribution of cisTopics and explore the nature and regulatory proteins driving them.
Magrittr provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, "Ceci n'est pas un pipe."
This package provides a toolkit for all URL-handling needs, including encoding and decoding, parsing, parameter extraction and modification. All functions are designed to be both fast and entirely vectorized. It is intended to be useful for people dealing with web-related datasets, such as server-side logs, although may be useful for other situations involving large sets of URLs.
This package is a usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. The package is also designed as connector to the cluster management tool sfCluster, but can also used without it.
This package provides a differential evolution (DE) stochastic algorithms for global optimization of problems with and without constraints. The aim is to curate a collection of its state-of-the-art variants that
do not sacrifice simplicity of design,
are essentially tuning-free, and
can be efficiently implemented directly in the R language.
STFU-8 is a hacky text encoding/decoding protocol for files that partially uses UTF-8. Its primary purpose is to allow a human to visualize and edit data that is mostly UTF-8. It will encode all non-UTF8-compliant bytes as longform text (e.g., ESC becomes r\x1B) and tries to encode ill-formed UTF-8.
This package provides a quick method for visualizing non-aggregated line-list or aggregated census data stratified by age and one or two categorical variables (e.g. gender and health status) with any number of values. It returns a ggplot object, allowing the user to further customize the output. This package is part of the R4Epis project <https://r4epis.netlify.app/>.
This package provides a variable selection method using B-Splines in multivariate nOnparametric Regression models Based on partial dErivatives Regularization (ABSORBER) implements a novel variable selection method in a nonlinear multivariate model using B-splines. For further details we refer the reader to the paper Savino, M. E. and Lévy-Leduc, C. (2024), <https://hal.science/hal-04434820>.
It performs All-Resolutions Inference (ARI) on functional Magnetic Resonance Image (fMRI) data. As a main feature, it estimates lower bounds for the proportion of active voxels in a set of clusters as, for example, given by a cluster-wise analysis. The method is described in Rosenblatt, Finos, Weeda, Solari, Goeman (2018) <doi:10.1016/j.neuroimage.2018.07.060>.