|
r-eml
|
public |
Work with Ecological Metadata Language ('EML') files. 'EML' is a widely used metadata standard in the ecological and environmental sciences, described in Jones et al. (2006), <doi:10.1146/annurev.ecolsys.37.091305.110031>.
|
2025-09-22 |
|
tango-database
|
public |
Tango Database Server
|
2025-09-22 |
|
r-riskclustr
|
public |
A collection of functions related to the study of etiologic heterogeneity both across disease subtypes and across individual disease markers. The included functions allow one to quantify the extent of etiologic heterogeneity in the context of a case-control study, and provide p-values to test for etiologic heterogeneity across individual risk factors. Begg CB, Zabor EC, Bernstein JL, Bernstein L, Press MF, Seshan VE (2013) <doi: 10.1002/sim.5902>.
|
2025-09-22 |
|
r-lmms
|
public |
Linear Mixed effect Model Splines ('lmms') implements linear mixed effect model splines for modelling and differential expression for highly dimensional data sets: investNoise() for quality control and filterNoise() for removing non-informative trajectories; lmmSpline() to model time course expression profiles and lmmsDE() performs differential expression analysis to identify differential expression between groups, time and/or group x time interaction.
|
2025-09-22 |
|
r-kdetrees
|
public |
A non-parametric method for identifying potential outlying observations in a collection of phylogenetic trees based on the methods of Owen and Provan (2011). Such discordant trees may indicate problems with sequence annotation or tree reconstruction, or they may represent interesting biological phenomena, such as horizontal gene transfers.
|
2025-09-22 |
|
ovito
|
public |
Scientific visualization and analysis software for atomistic simulation data
|
2025-09-22 |
|
r-osfr
|
public |
An interface for interacting with 'OSF' (<https://osf.io>). 'osfr' enables you to access open research materials and data, or create and manage your own private or public projects.
|
2025-09-22 |
|
r-skellam
|
public |
Functions for the Skellam distribution, including: density (pmf), cdf, quantiles and regression.
|
2025-09-22 |
|
r-prettymapr
|
public |
Automates the process of creating a scale bar and north arrow in any package that uses base graphics to plot in R. Bounding box tools help find and manipulate extents. Finally, there is a function to automate the process of setting margins, plotting the map, scale bar, and north arrow, and resetting graphic parameters upon completion.
|
2025-09-22 |
|
r-mcmcprecision
|
public |
Estimates the precision of transdimensional Markov chain Monte Carlo (MCMC) output, which is often used for Bayesian analysis of models with different dimensionality (e.g., model selection). Transdimensional MCMC (e.g., reversible jump MCMC) relies on sampling a discrete model-indicator variable to estimate the posterior model probabilities. If only few switches occur between the models, precision may be low and assessment based on the assumption of independent samples misleading. Based on the observed transition matrix of the indicator variable, the method of Heck, Overstall, Gronau, & Wagenmakers (2018, Statistics & Computing) <doi:10.1007/s11222-018-9828-0> draws posterior samples of the stationary distribution to (a) assess the uncertainty in the estimated posterior model probabilities and (b) estimate the effective sample size of the MCMC output.
|
2025-09-22 |
|
rbspy
|
public |
Sampling profiler for Ruby
|
2025-09-22 |
|
r-r62s3
|
public |
After defining an R6 class, R62S3 is used to automatically generate optional S3/S4 generics and methods for dispatch. Also allows piping for R6 objects.
|
2025-09-22 |
|
r-cffr
|
public |
The Citation File Format version 1.2.0 <doi:10.5281/zenodo.5171937> is a human and machine readable file format which provides citation metadata for software. This package provides core utilities to generate and validate this metadata.
|
2025-09-22 |
|
r-geojsonlint
|
public |
Tools for linting 'GeoJSON'. Includes tools for interacting with the online tool <http://geojsonlint.com>, the 'Javascript' library 'geojsonhint' (<https://www.npmjs.com/package/geojsonhint>), and validating against a 'GeoJSON' schema via the 'Javascript' library (<https://www.npmjs.com/package/is-my-json-valid>). Some tools work locally while others require an internet connection.
|
2025-09-22 |
|
armadillo
|
public |
Armadillo C++ linear algebra library
|
2025-09-22 |
|
odetoolbox
|
public |
ODE-toolbox: Automatic selection and generation of integration schemes
|
2025-09-22 |
|
r-emld
|
public |
This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.
|
2025-09-22 |
|
r-rmzqc
|
public |
Reads, writes and validates 'mzQC' files. The 'mzQC' format is a standardized file format for the exchange, transmission, and archiving of quality metrics derived from biological mass spectrometry data, as defined by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative) Quality Control working group. See <https://hupo-psi.github.io/mzQC/> for details.
|
2025-09-22 |
|
r-poiclaclu
|
public |
Implements the methods described in the paper, Witten (2011) Classification and Clustering of Sequencing Data using a Poisson Model, Annals of Applied Statistics 5(4) 2493-2518.
|
2025-09-22 |
|
r-btyd
|
public |
Functions for data preparation, parameter estimation, scoring, and plotting for the BG/BB (Fader, Hardie, and Shang 2010 <doi:10.1287/mksc.1100.0580>), BG/NBD (Fader, Hardie, and Lee 2005 <doi:10.1287/mksc.1040.0098>) and Pareto/NBD and Gamma/Gamma (Fader, Hardie, and Lee 2005 <doi:10.1509/jmkr.2005.42.4.415>) models.
|
2025-09-22 |
|
r-ptw
|
public |
Parametric Time Warping aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). Both warping of peak profiles and of peak lists are supported.
|
2025-09-22 |
|
hdx-python-country
|
public |
Utilities to map between country and region codes and names, and to match
administrative level names from different sources
|
2025-09-22 |
|
deepspeed
|
public |
DeepSpeed library
|
2025-09-22 |
|
r-nodbi
|
public |
Simplified document database access and manipulation, providing a common API across supported 'NoSQL' databases 'Elasticsearch', 'CouchDB', 'MongoDB' as well as 'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
|
2025-09-22 |
|
r-shinyalert
|
public |
Easily create pretty popup messages (modals) in 'Shiny'. A modal can contain text, images, OK/Cancel buttons, an input to get a response from the user, and many more customizable options.
|
2025-09-22 |
