Showing 20 of total 20 results (show query)
cynkra
fledge:Smoother Change Tracking and Versioning for R Packages
Streamlines the process of updating changelogs (NEWS.md) and versioning R packages developed in git repositories.
Maintained by Kirill Müller. Last updated 3 months ago.
11.5 match 188 stars 8.73 score 10 scripts
ebird
ebirdst:Access and Analyze eBird Status and Trends Data Products
Tools for accessing and analyzing eBird Status and Trends Data Products (<https://science.ebird.org/en/status-and-trends>). eBird (<https://ebird.org/home>) is a global database of bird observations collected by member of the public. eBird Status and Trends uses these data to model global bird distributions, abundances, and population trends at a high spatial and temporal resolution.
Maintained by Matthew Strimas-Mackey. Last updated 1 months ago.
8.9 match 26 stars 8.77 score 228 scripts
kapsner
autonewsmd:Auto-Generate Changelog using Conventional Commits
Automatically generate a changelog file (NEWS.md / CHANGELOG.md) from the git history using conventional commit messages (<https://www.conventionalcommits.org/en/v1.0.0/>).
Maintained by Lorenz A. Kapsner. Last updated 6 months ago.
automationchangelog-generatorconventional-commits
13.0 match 13 stars 5.81 score 7 scripts
rkoenker
quantreg:Quantile Regression
Estimation and inference methods for models for conditional quantile functions: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press, <doi:10.1017/CBO9780511754098> and Koenker, R. et al. (2017) Handbook of Quantile Regression, CRC Press, <doi:10.1201/9781315120256>.
Maintained by Roger Koenker. Last updated 23 days ago.
5.3 match 18 stars 13.93 score 2.6k scripts 1.5k dependents
juba
obsplot:Create Charts with 'Observable Plot'
Creation of charts with the 'Observable Plot' 'JavaScript' library.
Maintained by Julien Barnier. Last updated 2 years ago.
10.3 match 60 stars 5.08 score 10 scripts
vimc
orderly:Lightweight Reproducible Reporting
Order, create and store reports from R. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.
Maintained by Rich FitzJohn. Last updated 2 years ago.
5.3 match 117 stars 9.63 score 94 scripts 4 dependents
undocumeantit
roxyPackage:Utilities to Automate Package Builds
The intention of this package is to make packaging R code as easy as possible. 'roxyPackage' uses tools from the 'roxygen2' package to generate documentation. It also automatically generates and updates files like *-package.R, DESCRIPTION, CITATION, ChangeLog and NEWS.Rd. Building packages supports source format, as well as several binary formats (MS Windows, Mac OS X, Debian GNU/Linux) if the package contains pure R code only. The packages built are stored in a fully functional local R package repository which can be synced to a web server to share them with others. This includes the generation of browsable HTML pages similar to CRAN, with support for RSS feeds from the ChangeLog. Please read the vignette for a more detailed explanation by example.
Maintained by m.eik michalke. Last updated 8 months ago.
12.8 match 11 stars 3.74 score 1 scripts
bioc
limma:Linear Models for Microarray and Omics Data
Data analysis, linear models and differential expression for omics data.
Maintained by Gordon Smyth. Last updated 4 days ago.
exonarraygeneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentdataimportbayesianclusteringregressiontimecoursemicroarraymicrornaarraymrnamicroarrayonechannelproprietaryplatformstwochannelsequencingrnaseqbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrolbiomedicalinformaticscellbiologycheminformaticsepigeneticsfunctionalgenomicsgeneticsimmunooncologymetabolomicsproteomicssystemsbiologytranscriptomics
3.3 match 13.84 score 16k scripts 587 dependents
lrberge
fixest:Fast Fixed-Effects Estimations
Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial. The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://github.com/lrberge/fixest/blob/master/_DOCS/FENmlm_paper.pdf>. Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.
Maintained by Laurent Berge. Last updated 7 months ago.
2.2 match 394 stars 14.69 score 3.8k scripts 26 dependents
roelandkindt
BiodiversityR:Package for Community Ecology and Suitability Analysis
Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Maintained by Roeland Kindt. Last updated 2 months ago.
4.3 match 17 stars 7.13 score 390 scripts 2 dependents
sherrillmix
taxonomizr:Functions to Work with NCBI Accessions and Taxonomy
Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.
Maintained by Scott Sherrill-Mix. Last updated 20 days ago.
2.2 match 72 stars 8.85 score 255 scripts 2 dependentsbioc
TRONCO:TRONCO, an R package for TRanslational ONCOlogy
The TRONCO (TRanslational ONCOlogy) R package collects algorithms to infer progression models via the approach of Suppes-Bayes Causal Network, both from an ensemble of tumors (cross-sectional samples) and within an individual patient (multi-region or single-cell samples). The package provides parallel implementation of algorithms that process binary matrices where each row represents a tumor sample and each column a single-nucleotide or a structural variant driving the progression; a 0/1 value models the absence/presence of that alteration in the sample. The tool can import data from plain, MAF or GISTIC format files, and can fetch it from the cBioPortal for cancer genomics. Functions for data manipulation and visualization are provided, as well as functions to import/export such data to other bioinformatics tools for, e.g, clustering or detection of mutually exclusive alterations. Inferred models can be visualized and tested for their confidence via bootstrap and cross-validation. TRONCO is used for the implementation of the Pipeline for Cancer Inference (PICNIC).
Maintained by Luca De Sano. Last updated 6 days ago.
biomedicalinformaticsbayesiangraphandnetworksomaticmutationnetworkinferencenetworkclusteringdataimportsinglecellimmunooncologyalgorithmscancer-inferencetumors
2.2 match 30 stars 8.35 score 38 scriptsbioc
SparseSignatures:SparseSignatures
Point mutations occurring in a genome can be divided into 96 categories based on the base being mutated, the base it is mutated into and its two flanking bases. Therefore, for any patient, it is possible to represent all the point mutations occurring in that patient's tumor as a vector of length 96, where each element represents the count of mutations for a given category in the patient. A mutational signature represents the pattern of mutations produced by a mutagen or mutagenic process inside the cell. Each signature can also be represented by a vector of length 96, where each element represents the probability that this particular mutagenic process generates a mutation of the 96 above mentioned categories. In this R package, we provide a set of functions to extract and visualize the mutational signatures that best explain the mutation counts of a large number of patients.
Maintained by Luca De Sano. Last updated 7 days ago.
biomedicalinformaticssomaticmutation
2.2 match 11 stars 6.42 score 4 scripts
emilio-berti
enerscape:Compute Energy Landscapes
Compute energy landscapes using a digital elevation model raster and body mass of animals.
Maintained by Emilio Berti. Last updated 7 months ago.
2.2 match 4 stars 4.68 score 12 scriptsbioc
RESOLVE:RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes
Cancer is a genetic disease caused by somatic mutations in genes controlling key biological functions such as cellular growth and division. Such mutations may arise both through cell-intrinsic and exogenous processes, generating characteristic mutational patterns over the genome named mutational signatures. The study of mutational signatures have become a standard component of modern genomics studies, since it can reveal which (environmental and endogenous) mutagenic processes are active in a tumor, and may highlight markers for therapeutic response. Mutational signatures computational analysis presents many pitfalls. First, the task of determining the number of signatures is very complex and depends on heuristics. Second, several signatures have no clear etiology, casting doubt on them being computational artifacts rather than due to mutagenic processes. Last, approaches for signatures assignment are greatly influenced by the set of signatures used for the analysis. To overcome these limitations, we developed RESOLVE (Robust EStimation Of mutationaL signatures Via rEgularization), a framework that allows the efficient extraction and assignment of mutational signatures. RESOLVE implements a novel algorithm that enables (i) the efficient extraction, (ii) exposure estimation, and (iii) confidence assessment during the computational inference of mutational signatures.
Maintained by Luca De Sano. Last updated 7 days ago.
biomedicalinformaticssomaticmutation
2.2 match 1 stars 4.60 score 3 scripts
pauljohn32
kutils:Project Management Tools
Tools for data importation, recoding, and inspection. There are functions to create new project folders, R code templates, create uniquely named output directories, and to quickly obtain a visual summary for each variable in a data frame. The main feature here is the systematic implementation of the "variable key" framework for data importation and recoding. We are eager to have community feedback about the variable key and the vignette about it. In version 1.7, the function 'semTable' is removed. It was deprecated since 1.67. That is provided in a separate package, 'semTable'.
Maintained by Paul Johnson. Last updated 2 years ago.
1.6 match 5.85 score 110 scripts 20 dependentslrberge
fplot:Automatic Distribution Graphs Using Formulas
Easy way to plot regular/weighted/conditional distributions by using formulas. The core of the package concerns distribution plots which are automatic: the many options are tailored to the data at hand to offer the nicest and most meaningful graphs possible -- with no/minimum user input. Further provide functions to plot conditional trends and box plots. See <https://lrberge.github.io/fplot/> for more information.
Maintained by Laurent Berge. Last updated 2 years ago.
2.2 match 16 stars 4.20 score 10 scripts
agdamsbo
stRoke:Clinical Stroke Research
A collection of tools for clinical trial data management and analysis in research and teaching. The package is mainly collected for personal use, but any use beyond that is encouraged. This package has migrated functions from 'agdamsbo/daDoctoR', and new functions has been added. Version follows months and year. See NEWS/Changelog for release notes. This package includes sampled data from the TALOS trial (Kraglund et al (2018) <doi:10.1161/STROKEAHA.117.020067>). The win_prob() function is based on work by Zou et al (2022) <doi:10.1161/STROKEAHA.121.037744>. The age_calc() function is based on work by Becker (2020) <doi:10.18637/jss.v093.i02>.
Maintained by Andreas Gammelgaard Damsbo. Last updated 5 months ago.
0.5 match 4.18 score 7 scripts