Showing 116 of total 116 results (show query)
tomkellygenetics
vioplot:Violin Plot
A violin plot is a combination of a box plot and a kernel density plot. This package allows extensive customisation of violin plots.
Maintained by S. Thomas Kelly. Last updated 20 days ago.
boxplotcolourscustomisationdatavizformulaplottingviolin-plotviolinplotvioplot
25.9 match 26 stars 12.32 score 2.0k scripts 8 dependents
jameslairdsmith
customiser:Use R Markdown to Write your "Rprofile"
A simple way to write ".Rprofile" code in an R Markdown file and have it knit to the correct location for your operating system.
Maintained by James Laird-Smith. Last updated 8 months ago.
53.0 match 1 stars 3.18 score 1 scripts
finlaycampbell
outbreaker2:Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
Bayesian reconstruction of disease outbreaks using epidemiological and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F, Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.
Maintained by Finlay Campbell. Last updated 6 months ago.
10.2 match 7.67 score 101 scripts 1 dependents
r-lib
pkgdown:Make Static HTML Documentation for a Package
Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.
Maintained by Hadley Wickham. Last updated 9 hours ago.
3.8 match 734 stars 18.47 score 588 scripts 162 dependents
edzer
sp:Classes and Methods for Spatial Data
Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc. From this version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all, see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.
Maintained by Edzer Pebesma. Last updated 2 months ago.
3.0 match 127 stars 18.63 score 35k scripts 1.3k dependents
inlabru-org
inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions
Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.
Maintained by Finn Lindgren. Last updated 3 days ago.
4.4 match 96 stars 12.62 score 832 scripts 6 dependents
rstudio
rsconnect:Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io', and 'RPubs'
Programmatic deployment interface for 'RPubs', 'shinyapps.io', and 'Posit Connect'. Supported content types include R Markdown documents, Shiny applications, Plumber APIs, plots, and static web content.
Maintained by Aron Atkins. Last updated 15 days ago.
3.3 match 139 stars 14.90 score 3.1k scripts 6 dependents
neilstats
ckbplotr:Create CKB Plots
ckbplotr provides functions to help create and style plots in R. It is being developed by, and primarily for, China Kadoorie Biobank researchers.
Maintained by Neil Wright. Last updated 2 months ago.
7.8 match 10 stars 5.87 score 37 scripts
ropensci
visdat:Preliminary Visualisation of Data
Create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using 'ggplot2'.
Maintained by Nicholas Tierney. Last updated 8 months ago.
exploratory-data-analysismissingnesspeer-reviewedropenscivisualisation
3.1 match 452 stars 13.31 score 2.1k scripts 11 dependents
bioc
DAPAR:Tools for the Differential Analysis of Proteins Abundance with R
The package DAPAR is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required (see `Prostar` package).
Maintained by Samuel Wieczorek. Last updated 5 months ago.
proteomicsnormalizationpreprocessingmassspectrometryqualitycontrolgodataimportprostar1
7.3 match 2 stars 5.42 score 22 scripts 1 dependents
gadget-framework
gadget3:Globally-Applicable Area Disaggregated General Ecosystem Toolbox V3
A framework to assist creation of marine ecosystem models, generating either 'R' or 'C++' code which can then be optimised using the 'TMB' package and standard 'R' tools. Principally designed to reproduce gadget2 models in 'TMB', but can be extended beyond gadget2's capabilities. Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell (2016) <doi:10.18637/jss.v070.i05> "TMB: Automatic Differentiation and Laplace Approximation.". Begley, J., & Howell, D. (2004) <https://core.ac.uk/download/pdf/225936648.pdf> "An overview of Gadget, the globally applicable area-disaggregated general ecosystem toolbox. ICES.".
Maintained by Jamie Lentin. Last updated 30 days ago.
3.8 match 8 stars 8.66 score 170 scriptsropensci
opencage:Geocode with the OpenCage API
Geocode with the OpenCage API, either from place name to longitude and latitude (forward geocoding) or from longitude and latitude to the name and address of a location (reverse geocoding), see <https://opencagedata.com>.
Maintained by Daniel Possenriede. Last updated 2 months ago.
geocodegeocoderopencageopencage-apiopencage-geocoderpeer-reviewedplacenamesrspatial
3.8 match 87 stars 8.39 score 79 scripts
andrewcparnell
simmr:A Stable Isotope Mixing Model
Fits Stable Isotope Mixing Models (SIMMs) and is meant as a longer term replacement to the previous widely-used package SIAR. SIMMs are used to infer dietary proportions of organisms consuming various food sources from observations on the stable isotope values taken from the organisms' tissue samples. However SIMMs can also be used in other scenarios, such as in sediment mixing or the composition of fatty acids. The main functions are simmr_load() and simmr_mcmc(). The two vignettes contain a quick start and a full listing of all the features. The methods used are detailed in the papers Parnell et al 2010 <doi:10.1371/journal.pone.0009672>, and Parnell et al 2013 <doi:10.1002/env.2221>.
Maintained by Emma Govan. Last updated 11 months ago.
4.1 match 31 stars 7.58 score 81 scripts
andrewljackson
SIBER:Stable Isotope Bayesian Ellipses in R
Fits bi-variate ellipses to stable isotope data using Bayesian inference with the aim being to describe and compare their isotopic niche.
Maintained by Andrew Jackson. Last updated 10 months ago.
community-ecologyecologyniche-modellingstable-isotopesjagscpp
3.3 match 36 stars 9.13 score 187 scripts 1 dependents
alxsrobert
o2geosocial:Reconstruction of Transmission Chains from Surveillance Data
Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. (2020) <doi:10.1098/rsif.2020.0084>).
Maintained by Alexis Robert. Last updated 9 months ago.
baysian-inferencemarkov-chain-monte-carlotransmission-chain-reconstructioncpp
5.9 match 8 stars 4.90 score 5 scripts
cmlmagneville
mFD:Compute and Illustrate the Multiple Facets of Functional Diversity
Computing functional traits-based distances between pairs of species for species gathered in assemblages allowing to build several functional spaces. The package allows to compute functional diversity indices assessing the distribution of species (and of their dominance) in a given functional space for each assemblage and the overlap between assemblages in a given functional space, see: Chao et al. (2018) <doi:10.1002/ecm.1343>, Maire et al. (2015) <doi:10.1111/geb.12299>, Mouillot et al. (2013) <doi:10.1016/j.tree.2012.10.004>, Mouillot et al. (2014) <doi:10.1073/pnas.1317625111>, Ricotta and Szeidl (2009) <doi:10.1016/j.tpb.2009.10.001>. Graphical outputs are included. Visit the 'mFD' website for more information, documentation and examples.
Maintained by Camille Magneville. Last updated 3 months ago.
3.8 match 26 stars 7.35 score 61 scripts
sakk-statistics
survSAKK:Create Publication Ready Kaplan-Meier Plots
Incorporate various statistics and layout customization options to enhance the efficiency and adaptability of the Kaplan-Meier plots.
Maintained by Katrin Gysel. Last updated 2 months ago.
5.7 match 1 stars 4.81 score 10 scripts
teunbrand
ggarrow:Arrows for 'ggplot2'
A 'ggplot2' extension that adds specialised arrow geometry layers. It offers more arrow options than the standard 'grid' arrows that are built-in many line-based geom layers.
Maintained by Teun van den Brand. Last updated 9 months ago.
ggplot-extensionggplot2ggplot2-geom
3.8 match 54 stars 7.17 score 61 scripts 1 dependents
acorg
Racmacs:Antigenic Cartography Macros
A toolkit for making antigenic maps from immunological assay data, in order to quantify and visualize antigenic differences between different pathogen strains as described in Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World Health Organization influenza vaccine strain selection process. Additional functions allow for the diagnostic evaluation of antigenic maps and an interactive viewer is provided to explore antigenic relationships amongst several strains and incorporate the visualization of associated genetic information.
Maintained by Sam Wilks. Last updated 9 months ago.
3.3 match 21 stars 8.06 score 362 scripts
hidef-aerial-surveying
stochLAB:Stochastic Collision Risk Model
Collision Risk Models for avian fauna (seabird and migratory birds) at offshore wind farms. The base deterministic model is derived from Band (2012) <https://tethys.pnnl.gov/publications/using-collision-risk-model-assess-bird-collision-risks-offshore-wind-farms>. This was further expanded on by Masden (2015) <doi:10.7489/1659-1> and code used here is heavily derived from this work with input from Dr A. Cook at the British Trust for Ornithology. These collision risk models are useful for marine ornithologists who are working in the offshore wind industry, particularly in UK waters. However, many of the species included in the stochastic collision risk models (stoch_crm) can also be found in the North Atlantic in the United States and Canada, and could be applied there.
Maintained by Grant Humphries. Last updated 2 years ago.
collision-riskmigratoryspeciesoffshore-windseabirds
5.5 match 6 stars 4.78 score 10 scripts
tmlange
optRF:Optimising Random Forest Stability by Determining the Optimal Number of Trees
Calculating the stability of random forest with certain numbers of trees. The non-linear relationship between stability and numbers of trees is described using a logistic regression model and used to estimate the optimal number of trees.
Maintained by Thomas Martin Lange. Last updated 1 months ago.
5.4 match 4.78 score
nik01010
dashboardthemes:Customise the Appearance of 'shinydashboard' Applications using Themes
Allows manual creation of themes and logos to be used in applications created using the 'shinydashboard' package. Removes the need to change the underlying css code by wrapping it into a set of convenient R functions.
Maintained by Nik Lilovski. Last updated 3 years ago.
2.9 match 314 stars 8.60 score 424 scripts 2 dependents
msberends
plot2:A Plotting Assistant for Fast 'ggplot2' Visualisations
A streamlined extension of 'ggplot2' designed to simplify and accelerate the creation of data visualisations. 'plot2' automates common tasks such as axis handling, plot type selection, and data transformation, allowing users to create complex, publication-ready plots with minimal code. It integrates seamlessly with the tidyverse and retains full compatibility with 'ggplot2', while offering additional conveniences like enhanced sorting, faceting, and custom theming.
Maintained by Matthijs S. Berends. Last updated 7 days ago.
ggplot2helperplottingtidyverse
5.7 match 1 stars 4.32 score 8 scripts 1 dependents
jiscah
sequoia:Pedigree Inference from SNPs
Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.
Maintained by Jisca Huisman. Last updated 9 months ago.
pedigreepedigree-reconstructionpedigreessequoiasnpsnp-datafortran
3.3 match 26 stars 7.40 score 79 scripts
myles-lewis
locuszoomr:Gene Locus Plot with Gene Annotations
Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Maintained by Myles Lewis. Last updated 13 days ago.
3.2 match 40 stars 7.43 score 50 scripts
dereckmezquita
stenographer:Flexible and Customisable Logging System
A comprehensive logging framework for R applications that provides hierarchical logging levels, database integration, and contextual logging capabilities. The package supports 'SQLite' storage for persistent logs, provides colour-coded console output for better readability, includes parallel processing support, and implements structured error reporting with 'JSON' formatting.
Maintained by Dereck Mezquita. Last updated 2 months ago.
4.6 match 3 stars 5.08 score 1 scripts
selkamand
assertions:Simple Assertions for Beautiful and Customisable Error Messages
Provides simple assertions with sensible defaults and customisable error messages. It offers convenient assertion call wrappers and a general assert function that can handle any condition. Default error messages are user friendly and easily customized with inline code evaluation and styling powered by the 'cli' package.
Maintained by Sam El-Kamand. Last updated 4 months ago.
3.4 match 3 stars 6.84 score 172 scripts 3 dependents
computationalstylistics
tidystopwords:Customisable Stop-Words in 110 Languages
Functions to generate stop-word lists in 110 languages, in a way consistent across all the languages supported. The generated lists are based on the morphological tagset from the Universal Dependencies.
Maintained by Maciej Eder. Last updated 12 months ago.
4.8 match 6 stars 4.48 score 7 scripts
johncoene
sever:Customise 'Shiny' Disconnected Screens and Error Messages
Customise 'Shiny' disconnected screens as well as sanitize error messages to make them clearer and friendlier to the user.
Maintained by John Coene. Last updated 12 months ago.
3.5 match 78 stars 5.96 score 78 scripts 1 dependents
davidhodge931
ggblanket:Simplify 'ggplot2' Visualisation
Simplify 'ggplot2' visualisation with 'ggblanket' wrapper functions.
Maintained by David Hodge. Last updated 5 days ago.
data-visualisationdata-visualizationggplotggplot-extensionggplot2ggplot2-enhancementsvisualisationvisualization
2.3 match 170 stars 8.43 score 45 scripts
ellessenne
KMunicate:KMunicate-Style Kaplan–Meier Plots
Produce Kaplan–Meier plots in the style recommended following the KMunicate study by Morris et al. (2019) <doi:10.1136/bmjopen-2019-030215>. The KMunicate style consists of Kaplan-Meier curves with confidence intervals to quantify uncertainty and an extended risk table (per treatment arm) depicting the number of study subjects at risk, events, and censored observations over time. The resulting plots are built using 'ggplot2' and can be further customised to a certain extent, including themes, fonts, and colour scales.
Maintained by Alessandro Gasparini. Last updated 10 months ago.
4.0 match 7 stars 4.89 score 11 scriptsbioc
cytomapper:Visualization of highly multiplexed imaging data in R
Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.
Maintained by Lasse Meyer. Last updated 5 months ago.
immunooncologysoftwaresinglecellonechanneltwochannelmultiplecomparisonnormalizationdataimportbioimagingimaging-mass-cytometrysingle-cellspatial-analysis
2.0 match 32 stars 9.61 score 354 scripts 5 dependentsbioc
omXplore:Vizualization tools for 'omics' datasets with R
This package contains a collection of functions (written as shiny modules) for the visualisation and the statistical analysis of omics data. These plots can be displayed individually or embedded in a global Shiny module. Additionaly, it is possible to integrate third party modules to the main interface of the package omXplore.
Maintained by Samuel Wieczorek. Last updated 12 days ago.
softwareshinyappsmassspectrometrydatarepresentationguiqualitycontrolprostar2
3.5 match 5.40 score 23 scripts
natverse
nat:NeuroAnatomy Toolbox for Analysis of 3D Image Data
NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Maintained by Gregory Jefferis. Last updated 5 months ago.
3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation
1.9 match 67 stars 9.94 score 436 scripts 2 dependents
angabrio
missingHE:Missing Outcome Data in Health Economic Evaluation
Contains a suite of functions for health economic evaluations with missing outcome data. The package can fit different types of statistical models under a fully Bayesian approach using the software 'JAGS' (which should be installed locally and which is loaded in 'missingHE' via the 'R' package 'R2jags'). Three classes of models can be fitted under a variety of missing data assumptions: selection models, pattern mixture models and hurdle models. In addition to model fitting, 'missingHE' provides a set of specialised functions to assess model convergence and fit, and to summarise the statistical and economic results using different types of measures and graphs. The methods implemented are described in Mason (2018) <doi:10.1002/hec.3793>, Molenberghs (2000) <doi:10.1007/978-1-4419-0300-6_18> and Gabrio (2019) <doi:10.1002/sim.8045>.
Maintained by Andrea Gabrio. Last updated 2 years ago.
cost-effectiveness-analysishealth-economic-evaluationindividual-level-datajagsmissing-dataparametric-modellingsensitivity-analysiscpp
3.3 match 5 stars 5.38 score 24 scripts
ambiorix-web
ambiorix:Web Framework Inspired by 'Express.js'
A web framework inspired by 'express.js' to build any web service from multi-page websites to 'RESTful' application programming interfaces.
Maintained by John Coene. Last updated 11 hours ago.
2.3 match 212 stars 7.28 score 8 dependents
ndphillips
yarrr:A Companion to the e-Book "YaRrr!: The Pirate's Guide to R"
Contains a mixture of functions and data sets referred to in the introductory e-book "YaRrr!: The Pirate's Guide to R". The latest version of the e-book is available for free at <https://www.thepiratesguidetor.com>.
Maintained by Nathaniel Phillips. Last updated 12 months ago.
1.5 match 78 stars 10.67 score 1.2k scripts 2 dependents
mages
googleVis:R Interface to Google Charts
R interface to Google's chart tools, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection is required. The data remains local and is not uploaded to Google.
Maintained by Markus Gesmann. Last updated 10 months ago.
1.2 match 361 stars 12.98 score 2.4k scripts 11 dependents
carlosyanez
auspol:Australian Federal Election Results (2004-2022)
Retrieve Australian Federal Election results for House of Representatives and Senate, from 2004 onwards.
Maintained by Carlos Yáñez Santibáñez. Last updated 2 years ago.
auspolaustraliadataelectionspolitics
3.8 match 3.85 score 28 scripts
gpfda
GPFDA:Gaussian Process for Functional Data Analysis
Functionalities for modelling functional data with multidimensional inputs, multivariate functional data, and non-separable and/or non-stationary covariance structure of function-valued processes. In addition, there are functionalities for functional regression models where the mean function depends on scalar and/or functional covariates and the covariance structure depends on functional covariates. The development version of the package can be found on <https://github.com/gpfda/GPFDA-dev>.
Maintained by Evandro Konzen. Last updated 2 years ago.
3.6 match 1 stars 3.81 score 36 scripts 1 dependents
ai4ci
huxtableone:Descriptive Tables for Observational or Interventional Studies
Generating tabular summaries of data in a format suitable for reporting in journal articles is fiddly and slows down more detailed analysis. Comparing two populations with respect to an intervention, and reporting it is a task that can be largely automated.
Maintained by Robert Challen. Last updated 1 months ago.
4.1 match 3.30 score
stefanocoretta
speakr:A Wrapper for the Phonetic Software 'Praat'
It allows running 'Praat' scripts from R and it provides some wrappers for basic plotting. It also adds support for literate markdown tangling. The package is designed to bring reproducible phonetic research into R.
Maintained by Stefano Coretta. Last updated 9 days ago.
2.0 match 25 stars 6.63 score 19 scripts
cloudyr
googleComputeEngineR:R Interface with Google Compute Engine
Interact with the 'Google Compute Engine' API in R. Lets you create, start and stop instances in the 'Google Cloud'. Support for preconfigured instances, with templates for common R needs.
Maintained by Mark Edmondson. Last updated 13 hours ago.
apicloud-computingcloudyrgoogle-cloudgoogleauthrlaunching-virtual-machines
1.3 match 152 stars 9.73 score 235 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.
1.3 match 117 stars 9.63 score 94 scripts 4 dependentsandrewcparnell
Bchron:Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling
Enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); age-depth modelling as per the algorithm of Haslett and Parnell (2008) <DOI:10.1111/j.1467-9876.2008.00623.x>; Relative sea level rate estimation incorporating time uncertainty in polynomial regression models (Parnell and Gehrels 2015) <DOI:10.1002/9781118452547.ch32>; non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the Oxcal function SUM; currently unpublished), and reverse calibration of dates from calibrated into un-calibrated years (also unpublished).
Maintained by Andrew Parnell. Last updated 2 years ago.
1.5 match 36 stars 8.09 score 176 scripts 1 dependentsbioc
drawProteins:Package to Draw Protein Schematics from Uniprot API output
This package draws protein schematics from Uniprot API output. From the JSON returned by the GET command, it creates a dataframe from the Uniprot Features API. This dataframe can then be used by geoms based on ggplot2 and base R to draw protein schematics.
Maintained by Paul Brennan. Last updated 5 months ago.
visualizationfunctionalpredictionproteomics
1.3 match 34 stars 8.75 score 61 scripts 1 dependents
david-barnett
microViz:Microbiome Data Analysis and Visualization
Microbiome data visualization and statistics tools built upon phyloseq.
Maintained by David Barnett. Last updated 3 months ago.
microbiomemicrobiome-analysismicrobiota
1.9 match 114 stars 6.22 score 480 scripts
mattmar
rasterdiv:Diversity Indices for Numerical Matrices
Provides methods to calculate diversity indices on numerical matrices based on information theory, as described in Rocchini, Marcantonio and Ricotta (2017) <doi:10.1016/j.ecolind.2016.07.039>, and Rocchini et al. (2021) <doi:10.1101/2021.01.23.427872>.
Maintained by Matteo Marcantonio. Last updated 19 days ago.
1.5 match 15 stars 7.65 score 44 scripts 1 dependents
kcf-jackson
sketch:Interactive Sketches
Creates static / animated / interactive visualisations embeddable in R Markdown documents. It implements an R-to-JavaScript transpiler and enables users to write JavaScript applications using the syntax of R.
Maintained by Chun Fung Kwok. Last updated 1 years ago.
javascriptjstranspilervisualisation
2.0 match 125 stars 5.70 score 27 scriptsbioc
CrispRVariants:Tools for counting and visualising mutations in a target location
CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.
Maintained by Helen Lindsay. Last updated 5 months ago.
immunooncologycrisprgenomicvariationvariantdetectiongeneticvariabilitydatarepresentationvisualizationsequencing
2.0 match 5.51 score 32 scripts
dillonhammill
DataEditR:An Interactive Editor for Viewing, Entering, Filtering & Editing Data
An interactive editor built on 'rhandsontable' to allow the interactive viewing, entering, filtering and editing of data in R <https://dillonhammill.github.io/DataEditR/>.
Maintained by Dillon Hammill. Last updated 2 years ago.
1.5 match 385 stars 7.31 score 106 scripts
robjohnnoble
ggmuller:Create Muller Plots of Evolutionary Dynamics
Create plots that combine a phylogeny and frequency dynamics. Phylogenetic input can be a generic adjacency matrix or a tree of class "phylo". Inspired by similar plots in publications of the labs of RE Lenski and JE Barrick. Named for HJ Muller (who popularised such plots) and H Wickham (whose code this package exploits).
Maintained by Robert Noble. Last updated 1 years ago.
1.5 match 65 stars 7.29 score 50 scripts
modesto-escobar
netCoin:Interactive Analytic Networks
Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.
Maintained by Modesto Escobar. Last updated 16 days ago.
1.5 match 11 stars 7.22 score 47 scripts
darwin-eu
visOmopResults:Graphs and Tables for OMOP Results
Provides methods to transform omop_result objects into formatted tables and figures, facilitating the visualisation of study results working with the Observational Medical Outcomes Partnership (OMOP) Common Data Model.
Maintained by Núria Mercadé-Besora. Last updated 17 days ago.
1.3 match 7.73 score 53 scripts 4 dependents
devopifex
g2r:Interactive Grammar of Graphics
Interactive grammar of graphics.
Maintained by John Coene. Last updated 3 years ago.
2.3 match 119 stars 4.53 score 57 scripts
ald0405
SangerTools:Tools for Population Health Management Analytics
Created for population health analytics and monitoring. The functions in this package work best when working with patient level Master Patient Index-like datasets . Built to be used by NHS bodies and other health service providers.
Maintained by Asif Laldin. Last updated 1 years ago.
nhsnhs-r-communitypopulation-healthprevalence
2.0 match 5 stars 5.05 score 45 scripts
ggpmxdevelopment
ggPMX:'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models
At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling activities in order to reduce the overall effort required for generating such plots. For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox, called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP <doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>. When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required Chart Data instead of exporting it from the 'Monolix' gui.
Maintained by Matthew Fidler. Last updated 1 years ago.
1.3 match 39 stars 7.23 score 80 scriptstomkellygenetics
graphsim:Simulate Expression Data from 'igraph' Networks
Functions to develop simulated continuous data (e.g., gene expression) from a sigma covariance matrix derived from a graph structure in 'igraph' objects. Intended to extend 'mvtnorm' to take 'igraph' structures rather than sigma matrices as input. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. Here we present a versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from a multivariate normal distribution derived from a graph structure. This package allows the simulation of biological pathways from a graph structure based on a statistical model of gene expression. For example methods to infer biological pathways and gene regulatory networks from gene expression data can be tested on simulated datasets using this framework. This also allows for pathway structures to be considered as a confounding variable when simulating gene expression data to test the performance of genomic analyses.
Maintained by S. Thomas Kelly. Last updated 3 years ago.
benchmarkinggene-expressiongene-regulatory-networksgeneticsgenomic-data-analysisgenomicsgraph-algorithmsigraph-networksjossngs-analysissimulated-datasimulation-modeling
1.9 match 24 stars 5.08 score 2 scripts
rishvish
PieGlyph:Axis Invariant Scatter Pie Plots
Extends 'ggplot2' to help replace points in a scatter plot with pie-chart glyphs showing the relative proportions of different categories. The pie glyphs are independent of the axes and plot dimensions, to prevent distortions when the plot dimensions are changed.
Maintained by Rishabh Vishwakarma. Last updated 9 months ago.
1.3 match 5 stars 6.88 score 29 scripts 1 dependents
huizezhang-sherry
ferrn:Facilitate Exploration of touRR optimisatioN
Diagnostic plots for optimisation, with a focus on projection pursuit. These show paths the optimiser takes in the high-dimensional space in multiple ways: by reducing the dimension using principal component analysis, and also using the tour to show the path on the high-dimensional space. Several botanical colour palettes are included, reflecting the name of the package. A paper describing the methodology can be found at <https://journal.r-project.org/archive/2021/RJ-2021-105/index.html>.
Maintained by H. Sherry Zhang. Last updated 10 days ago.
1.8 match 6 stars 5.16 score 20 scripts
deepankardatta
blandr:Bland-Altman Method Comparison
Carries out Bland Altman analyses (also known as a Tukey mean-difference plot) as described by JM Bland and DG Altman in 1986 <doi:10.1016/S0140-6736(86)90837-8>. This package was created in 2015 as existing Bland-Altman analysis functions did not calculate confidence intervals. This package was created to rectify this, and create reproducible plots. This package is also available as a module for the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more information).
Maintained by Deepankar Datta. Last updated 9 months ago.
bland-altmanggplot2method-comparisonstatistics
1.3 match 22 stars 7.22 score 75 scriptsbioc
CCPlotR:Plots For Visualising Cell-Cell Interactions
CCPlotR is an R package for visualising results from tools that predict cell-cell interactions from single-cell RNA-seq data. These plots are generic and can be used to visualise results from multiple tools such as Liana, CellPhoneDB, NATMI etc.
Maintained by Sarah Ennis. Last updated 5 months ago.
singlecellnetworkvisualizationcellbiologysystemsbiology
1.5 match 43 stars 5.81 score 7 scripts
scholaempirica
reschola:The Schola Empirica Package
A collection of utilies, themes and templates for data analysis at Schola Empirica.
Maintained by Jan Netík. Last updated 5 months ago.
1.8 match 4 stars 4.83 score 14 scripts
epicentre-msf
epivis:Tools for visualising epidemiological data
Static visualisation of patient level linelist data.
Maintained by Paul Campbell. Last updated 5 months ago.
2.0 match 3 stars 4.13 score 3 scriptsteunbrand
ggh4x:Hacks for 'ggplot2'
A 'ggplot2' extension that does a variety of little helpful things. The package extends 'ggplot2' facets through customisation, by setting individual scales per panel, resizing panels and providing nested facets. Also allows multiple colour and fill scales per plot. Also hosts a smaller collection of stats, geoms and axis guides.
Maintained by Teun van den Brand. Last updated 3 months ago.
0.5 match 616 stars 13.98 score 4.4k scripts 20 dependents
crj32
Spectrum:Fast Adaptive Spectral Clustering for Single and Multi-View Data
A self-tuning spectral clustering method for single or multi-view data. 'Spectrum' uses a new type of adaptive density aware kernel that strengthens connections in the graph based on common nearest neighbours. It uses a tensor product graph data integration and diffusion procedure to integrate different data sources and reduce noise. 'Spectrum' uses either the eigengap or multimodality gap heuristics to determine the number of clusters. The method is sufficiently flexible so that a wide range of Gaussian and non-Gaussian structures can be clustered with automatic selection of K.
Maintained by Christopher R John. Last updated 5 years ago.
1.2 match 7 stars 5.99 score 47 scripts 1 dependents
cidm-ph
phylepic:Combined Visualisation of Phylogenetic and Epidemiological Data
A collection of utilities and 'ggplot2' extensions to assist with visualisations in genomic epidemiology. This includes the 'phylepic' chart, a visual combination of a phylogenetic tree and a matched epidemic curve. The included 'ggplot2' extensions such as date axes binned by week are relevant for other applications in epidemiology and beyond. The approach is described in Suster et al. (2024) <doi:10.1101/2024.04.02.24305229>.
Maintained by Carl Suster. Last updated 2 months ago.
genomicsgenomics-visualizationpublic-health
1.5 match 4.65 score 4 scripts
cran
ambiorix:Web Framework Inspired by 'Express.js'
A web framework inspired by 'express.js' to build any web service from multi-page websites to 'RESTful' application programming interfaces.
Maintained by John Coene. Last updated 14 hours ago.
2.3 match 3.08 score 8 dependents
lydialucchesi
smallsets:Visual Documentation for Data Preprocessing
Data practitioners regularly use the 'R' and 'Python' programming languages to prepare data for analyses. Thus, they encode important data preprocessing decisions in 'R' and 'Python' code. The 'smallsets' package subsequently decodes these decisions into a Smallset Timeline, a static, compact visualisation of data preprocessing decisions (Lucchesi et al. (2022) <doi:10.1145/3531146.3533175>). The visualisation consists of small data snapshots of different preprocessing steps. The 'smallsets' package builds this visualisation from a user's dataset and preprocessing code located in an 'R', 'R Markdown', 'Python', or 'Jupyter Notebook' file. Users simply add structured comments with snapshot instructions to the preprocessing code. One optional feature in 'smallsets' requires installation of the 'Gurobi' optimisation software and 'gurobi' 'R' package, available from <https://www.gurobi.com>. More information regarding the optional feature and 'gurobi' installation can be found in the 'smallsets' vignette.
Maintained by Lydia R. Lucchesi. Last updated 2 months ago.
data-sciencedata-visualizationdocumentation-toolmachine-learningpreprocessingpythonvisualization-tools
1.3 match 14 stars 5.19 score 11 scripts
pablocapilla
incR:Analysis of Incubation Data
Suite of functions to study animal incubation. At the core of incR lies an algorithm that allows for the scoring of incubation behaviour. Additionally, several functions extract biologically relevant metrics of incubation such as off-bout number and off-bout duration - for a review of avian incubation studies, see Nests, Eggs, and Incubation: New ideas about avian reproduction (2015) edited by D. Charles Deeming and S. James Reynolds <doi:10.1093/acprof:oso/9780198718666.001.0001>.
Maintained by Pablo Capilla-Lasheras. Last updated 3 months ago.
1.7 match 1 stars 3.70 score 9 scripts
cynthiahqy
ggtilematrix:Create customisable ggplot2 matrix
More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
Maintained by Cynthia Huang. Last updated 11 months ago.
3.1 match 2.00 score 3 scripts
baptiste
egg:Extensions for 'ggplot2': Custom Geom, Custom Themes, Plot Alignment, Labelled Panels, Symmetric Scales, and Fixed Panel Size
Miscellaneous functions to help customise 'ggplot2' objects. High-level functions are provided to post-process 'ggplot2' layouts and allow alignment between plot panels, as well as setting panel sizes to fixed values. Other functions include a custom 'geom', and helper functions to enforce symmetric scales or add tags to facetted plots.
Maintained by Baptiste Auguie. Last updated 4 years ago.
0.5 match 13 stars 11.84 score 2.4k scripts 67 dependents
sjtingle
rmsMD:Output Results from 'rms' Models for Medical Journals
This takes the output of models performed using the 'rms' package and returns a dataframe with the results. This output is in the format required by medical journals. For example for cox regression models, the hazard ratios, their 95% confidence intervals, and p values will be provided. There are additional functions for outputs when the model included restricted cubic spline (RCS) terms. Models using imputed data (eg from aregimpute()) and fitted used fit.mult.impute() can also be processed. The dataframe which is returned can easily be turned into a publication ready table with packages 'flextable' and 'officer'.
Maintained by Samuel Tingle. Last updated 9 days ago.
1.5 match 3.85 score
jared-fowler
prettyglm:Pretty Summaries of Generalized Linear Model Coefficients
One of the main advantages of using Generalised Linear Models is their interpretability. The goal of 'prettyglm' is to provide a set of functions which easily create beautiful coefficient summaries which can readily be shared and explained. 'prettyglm' helps users create coefficient summaries which include categorical base levels, variable importance and type III p.values. 'prettyglm' also creates beautiful relativity plots for categorical, continuous and splined coefficients.
Maintained by Jared Fowler. Last updated 1 years ago.
classificationclassification-modeldata-sciencedata-visualizationglmlinear-modelsregressionregression-analysisregression-modelregression-modelsstatistical-models
1.2 match 3 stars 4.73 score 36 scripts
airr-community
ogrdbstats:Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics
Multiple tools are now available for inferring the personalised germ line set from an adaptive immune receptor repertoire. Output from these tools is converted to a single format and supplemented with rich data such as usage and characterisation of 'novel' germ line alleles. This data can be particularly useful when considering the validity of novel inferences. Use of the analysis provided is described in <doi:10.3389/fimmu.2019.00435>.
Maintained by William Lees. Last updated 28 days ago.
1.3 match 1 stars 4.18 score 8 scripts
csdaw
ggprism:A 'ggplot2' Extension Inspired by 'GraphPad Prism'
Provides various themes, palettes, and other functions that are used to customise ggplots to look like they were made in 'GraphPad Prism'. The 'Prism'-look is achieved with theme_prism() and scale_fill|colour_prism(), axes can be changed with custom guides like guide_prism_minor(), and significance indicators added with add_pvalue().
Maintained by Charlotte Dawson. Last updated 12 months ago.
0.5 match 175 stars 10.56 score 1.1k scripts 5 dependentsbioc
gmoviz:Seamless visualization of complex genomic variations in GMOs and edited cell lines
Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. `gmoviz` provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale.
Maintained by Kathleen Zeglinski. Last updated 5 months ago.
visualizationsequencinggeneticvariabilitygenomicvariationcoverage
1.3 match 4.30 score 9 scripts
azure
AzureAuth:Authentication Services for Azure Active Directory
Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure. Part of the 'AzureR' family of packages.
Maintained by Hong Ooi. Last updated 3 years ago.
azureazure-active-directoryazure-sdk-roauth2
0.5 match 44 stars 10.42 score 57 scripts 23 dependents
jcdterry
bipartiteD3:Interactive Bipartite Graphs
Generates interactive bipartite graphs using the D3 library. Designed for use with the 'bipartite' analysis package. Includes open source 'viz-js' library Adapted from examples at <https://bl.ocks.org/NPashaP> (released under GPL-3).
Maintained by Chris Terry. Last updated 6 months ago.
1.5 match 3.36 score 23 scriptscran
DImodels:Diversity-Interactions (DI) Models
The 'DImodels' package is suitable for analysing data from biodiversity and ecosystem function studies using the Diversity-Interactions (DI) modelling approach introduced by Kirwan et al. (2009) <doi:10.1890/08-1684.1>. Suitable data will contain proportions for each species and a community-level response variable, and may also include additional factors, such as blocks or treatments. The package can perform data manipulation tasks, such as computing pairwise interactions (the DI_data() function), can perform an automated model selection process (the autoDI() function) and has the flexibility to fit a wide range of user-defined DI models (the DI() function).
Maintained by Rafael de Andrade Moral. Last updated 1 years ago.
1.2 match 4.19 score 52 scripts 2 dependents
remlapmot
knitexercise:Knit Exercise Questions and Solutions from the Same R Markdown Document
Provides a function to knit questions and solutions documents from the same R Markdown document.
Maintained by Tom Palmer. Last updated 23 days ago.
1.3 match 1 stars 3.81 score 1 scripts
finyang
lazybar:Progress Bar with Remaining Time Forecast Method
A simple progress bar showing estimated remaining time. Multiple forecast methods and user defined forecast method for the remaining time are supported.
Maintained by Yangzhuoran Yang. Last updated 5 years ago.
1.8 match 1 stars 2.70 score
terminological
ggrrr:Addressing Annoyances and Irritations
Visualisation hacks, tabular data helpers, fonts, caching, tidy data functions. It is an swiss army knife, jack of all trades.
Maintained by Robert Challen. Last updated 9 months ago.
1.7 match 1 stars 2.74 score 11 scriptscran
WoodSimulatR:Generate Simulated Sawn Timber Strength Grading Data
Tools for generating simulated sawn timber strength grading data with a main focus on statistical simulation based on covariance matrices. Simulation data for Norway spruce sawn timber from Austria and reference values of means and standard deviations of grade determining properties from literature for a number of European countries are provided, as well.
Maintained by Andreas Weidenhiller. Last updated 13 days ago.
1.5 match 2.70 score
modeloriented
modelStudio:Interactive Studio for Explanatory Model Analysis
Automate the explanatory analysis of machine learning predictive models. Generate advanced interactive model explanations in the form of a serverless HTML site with only one line of code. This tool is model-agnostic, therefore compatible with most of the black-box predictive models and frameworks. The main function computes various (instance and model-level) explanations and produces a customisable dashboard, which consists of multiple panels for plots with their short descriptions. It is possible to easily save the dashboard and share it with others. 'modelStudio' facilitates the process of Interactive Explanatory Model Analysis introduced in Baniecki et al. (2023) <doi:10.1007/s10618-023-00924-w>.
Maintained by Hubert Baniecki. Last updated 2 years ago.
aiexplainableexplainable-aiexplainable-machine-learningexplanatory-model-analysishumanimlinteractiveinteractivityinterpretabilityinterpretableinterpretable-machine-learninglearningmachinemodelmodel-visualizationvisualizationxai
0.5 match 330 stars 7.92 score 56 scripts
ggseg
ggseg3d:Tri-Surface Mesh Plots for Brain Atlases
Mainly contains a plotting function ggseg3d(), and data of two standard brain atlases (Desikan-Killiany and aseg). By far, the largest bit of the package is the data for each of the atlases. The functions and data enable users to plot tri-surface mesh plots of brain atlases, and customise these by projecting colours onto the brain segments based on values in their own data sets. Functions are wrappers for 'plotly'. Mowinckel & Vidal-Piñeiro (2020) <doi:10.1177/2515245920928009>.
Maintained by Athanasia Mo Mowinckel. Last updated 1 years ago.
0.5 match 36 stars 7.62 score 150 scripts 13 dependents
pmur002
gggrid:Draw with 'grid' in 'ggplot2'
An extension of 'ggplot2' that makes it easy to add raw 'grid' output, such as customised annotations, to a 'ggplot2' plot.
Maintained by Paul Murrell. Last updated 3 years ago.
0.5 match 35 stars 6.36 score 44 scripts 1 dependents
bioc
CluMSID:Clustering of MS2 Spectra for Metabolite Identification
CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.
Maintained by Tobias Depke. Last updated 5 months ago.
metabolomicspreprocessingclustering
0.5 match 10 stars 6.04 score 22 scriptsbioc
CAGEr:Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.
Maintained by Charles Plessy. Last updated 5 months ago.
preprocessingsequencingnormalizationfunctionalgenomicstranscriptiongeneexpressionclusteringvisualization
0.5 match 6.12 score 73 scripts
ashenoy-cmbi
grafify:Easy Graphs for Data Visualisation and Linear Models for ANOVA
Easily explore data by plotting graphs with a few lines of code. Use these ggplot() wrappers to quickly draw graphs of scatter/dots with box-whiskers, violins or SD error bars, data distributions, before-after graphs, factorial ANOVA and more. Customise graphs in many ways, for example, by choosing from colour blind-friendly palettes (12 discreet, 3 continuous and 2 divergent palettes). Use the simple code for ANOVA as ordinary (lm()) or mixed-effects linear models (lmer()), including randomised-block or repeated-measures designs, and fit non-linear outcomes as a generalised additive model (gam) using mgcv(). Obtain estimated marginal means and perform post-hoc comparisons on fitted models (via emmeans()). Also includes small datasets for practising code and teaching basics before users move on to more complex designs. See vignettes for details on usage <https://grafify.shenoylab.com/>. Citation: <doi:10.5281/zenodo.5136508>.
Maintained by Avinash R Shenoy. Last updated 17 hours ago.
ggplot2linear-modelspost-hoc-comparisonsstatisticsvignettes
0.5 match 48 stars 5.31 score 107 scripts
inzightvit
iNZightPlots:Graphical Tools for Exploring Data with 'iNZight'
Simple plotting function(s) for exploratory data analysis with flexible options allowing for easy plot customisation. The goal is to make it easy for beginners to start exploring a dataset through simple R function calls, as well as provide a similar interface to summary statistics and inference information. Includes functionality to generate interactive HTML-driven graphs. Used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions.
Maintained by Tom Elliott. Last updated 2 months ago.
0.5 match 2 stars 5.06 score 19 scripts 1 dependentsazure
AzureVM:Virtual Machines in 'Azure'
Functionality for working with virtual machines (VMs) in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/services/virtual-machines/>. Includes facilities to deploy, startup, shutdown, and cleanly delete VMs and VM clusters. Deployment configurations can be highly customised, and can make use of existing resources as well as creating new ones. A selection of predefined configurations is provided to allow easy deployment of commonly used Linux and Windows images, including Data Science Virtual Machines. With a running VM, execute scripts and install optional extensions. Part of the 'AzureR' family of packages.
Maintained by Hong Ooi. Last updated 2 years ago.
azureazure-sdk-razure-virtual-machinedata-science-virtual-machine
0.5 match 14 stars 5.05 score 16 scripts
chjackson
survextrap:Survival Extrapolation with a Flexible Parametric Model and External Data
Survival analysis using a flexible Bayesian model for individual-level right-censored data, optionally combined with aggregate data on counts of survivors in different periods of time. An M-spline is used to describe the hazard function, with a hierarchical prior on the coefficients to control overfitting. Proportional hazards or flexible non-proportional hazards models can be used to relate survival to predictors. Mixture cure models, additive hazards (relative survival) models and waning treatment effects models are also supported. Priors can be customised and calibrated to substantive beliefs. Posterior distributions are estimated using Stan, and outputs are arranged in a tidy format. See See Jackson (2023) <doi:10.48550/arXiv.2306.03957>.
Maintained by Christopher Jackson. Last updated 17 days ago.
0.5 match 10 stars 5.00 score 11 scripts
nunzioknerr
pannotator:Visualisation and Annotation of 360 Degree Imagery
Provides a customisable R 'shiny' app for immersively visualising, mapping and annotating panospheric (360 degree) imagery. The flexible interface allows annotation of any geocoded images using up to 4 user specified dropdown menus. The app uses 'leaflet' to render maps that display the geo-locations of images and panellum <https://pannellum.org/>, a lightweight panorama viewer for the web, to render images in virtual 360 degree viewing mode. Key functions include the ability to draw on & export parts of 360 images for downstream applications. Users can also draw polygons and points on map imagery related to the panoramic images and export them for further analysis. Downstream applications include using annotations to train Artificial Intelligence/Machine Learning (AI/ML) models and geospatial modelling and analysis of camera based survey data.
Maintained by Nunzio Knerr. Last updated 4 months ago.
0.5 match 2 stars 4.70 score 8 scripts
core-bioinformatics
bulkAnalyseR:Interactive Shiny App for Bulk Sequencing Data
Given an expression matrix from a bulk sequencing experiment, pre-processes it and creates a shiny app for interactive data analysis and visualisation. The app contains quality checks, differential expression analysis, volcano and cross plots, enrichment analysis and gene regulatory network inference, and can be customised to contain more panels by the user.
Maintained by Ilias Moutsopoulos. Last updated 1 years ago.
0.5 match 27 stars 4.47 score 11 scripts
gawainantell
divvy:Spatial Subsampling of Biodiversity Occurrence Data
Divide taxonomic occurrence data into geographic regions of fair comparison, with three customisable methods to standardise area and extent. Calculate common biodiversity and range-size metrics on subsampled data. Background theory and practical considerations for the methods are described in Antell and others (2023) <doi:10.31223/X5997Z>.
Maintained by Gawain Antell. Last updated 1 years ago.
0.5 match 4.00 score 10 scripts
pik-piam
brick:Building sector model with heterogeneous renovation and construction of the stock
This building stock model represents residential and commercial buildings at customisable regional and temporal resolution. The building stock is quantified in floor area and distinguished by building type (SFH/MFH) and location (rural/urban). In each building category, construction cohorts are tracked explicitly. This allows to characterise buildings specifically for each subset of buildings. The evolution of the building stock follows from the flows of constructed, renovated and demolished buildings and is optimised under cost minimisation with a benefit for heterogeneity in the choice of construction and renovation alternatives. This benefit captures heterogeneity in the preferences of the agents and the building structure.
Maintained by Robin Hasse. Last updated 20 days ago.
0.5 match 3.76 score 1 dependents
bradyajohnston
plasmapR:Create Plasmid Maps in R
Create circular plasmid maps as ggplot objects. Allows for parsing of .gb files and the creation of plasmid maps. Features allowing for customisation of aesthetics, like regular ggplot plots.
Maintained by Brady Johnston. Last updated 2 years ago.
0.5 match 83 stars 3.62 score 6 scripts
shahronak47
shinyRatings:An Intuitive Way of Providing Star Rating in a 'shiny' App
A simple interface to integrate star ratings into your 'shiny' apps. It can be used for customer feedback systems, user reviews, or any application that requires user ratings. 'shinyRatings' offers a straightforward and customisable solution that enhances user engagement and facilitates valuable feedback collection.
Maintained by Ronak Shah. Last updated 1 years ago.
0.5 match 8 stars 3.60 score 8 scripts
mrc-ide
rincewind:Utilities for processing forecasts matrices
This package contains utility functions for processing forecasts matrices.
Maintained by Sangeeta Bhatia. Last updated 3 years ago.
1.8 match 1 stars 1.00 score 1 scriptscran
reportRmd:Tidy Presentation of Clinical Reporting
Streamlined statistical reporting in 'Rmarkdown' environments. Facilitates the automated reporting of descriptive statistics, multiple univariate models, multivariable models and tables combining these outputs. Plotting functions include customisable survival curves, forest plots from logistic and ordinal regression and bivariate comparison plots.
Maintained by Lisa Avery. Last updated 2 months ago.
0.5 match 3.45 score 19 scripts 1 dependentscran
TrendSLR:Estimating Trend, Velocity and Acceleration from Sea Level Records
Analysis of annual average ocean water level time series, providing improved estimates of trend (mean sea level) and associated real-time velocities and accelerations. Improved trend estimates are based on singular spectrum analysis methods. Various gap-filling options are included to accommodate incomplete time series records. The package also includes a range of diagnostic tools to inspect the components comprising the original time series which enables expert interpretation and selection of likely trend components. A wide range of screen and plot to file options are available in the package.
Maintained by Phil J Watson. Last updated 6 years ago.
1.6 match 1.00 scorecynthiahqy
ggtilecal:Create static (and interactive) overview calendars using ggplot2
Creates tile-based calendar layouts using ggplot2 facets and tiles. Calculates calendar layout positioning variables, and generates customisable ggplot2 calendars for specified time periods and calendar units.
Maintained by Cynthia A. Huang. Last updated 9 months ago.
0.5 match 4 stars 3.08 score 6 scripts
r-forge
gridGraphviz:Drawing Graphs with 'grid'
Functions for drawing node-and-edge graphs that have been laid out by 'graphviz'. This provides an alternative rendering to that provided by the 'Rgraphviz' package, with two main advantages: the rendering provided by 'gridGraphviz' should be more similar to what 'graphviz' itself would draw; and rendering with 'grid' allows for post-hoc customisations using the named viewports and grobs that 'gridGraphviz' produces.
Maintained by Paul Murrell. Last updated 3 years ago.
0.5 match 2.78 score 2 scripts 1 dependentscran
XDNUTS:Discontinuous Hamiltonian Monte Carlo with Varying Trajectory Length
Hamiltonian Monte Carlo for both continuous and discontinuous posterior distributions with customisable trajectory length termination criterion. See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for the original Discontinuous Hamiltonian Monte Carlo, Hoffman et al. (2014) <doi:10.48550/arXiv.1111.4246> and Betancourt (2016) <doi:10.48550/arXiv.1601.00225> for the definition of possible Hamiltonian Monte Carlo termination criteria.
Maintained by Paolo Manildo. Last updated 2 months ago.
0.5 match 2.78 score
joe-chelladurai
starry:Explore Data with Plots and Tables
Provides modular functions and applications for quickly generating plots and tables. Each modular function opens a graphical user interface providing the user with options to create and customise plots and tables.
Maintained by Joe Chelladurai. Last updated 2 years ago.
0.5 match 1 stars 2.70 score 1 scripts
f-santi
noisyCE2:Cross-Entropy Optimisation of Noisy Functions
Cross-Entropy optimisation of unconstrained deterministic and noisy functions illustrated in Rubinstein and Kroese (2004, ISBN: 978-1-4419-1940-3) through a highly flexible and customisable function which allows user to define custom variable domains, sampling distributions, updating and smoothing rules, and stopping criteria. Several built-in methods and settings make the package very easy-to-use under standard optimisation problems.
Maintained by Flavio Santi. Last updated 4 years ago.
0.5 match 2.70 score 2 scripts
nutriverse
gnr:R Companion to the Global Nutrition Report
The Global Nutrition Report's purpose is to produce a single, authoritative source on progress toward addressing critical gaps in the nutrition accountability framework, both at national and international levels. This is a companion package to the Global Nutrition Report primarily for accessing the data used in the report and to reproduce the data visualisation produced in the report. This package contains functions that allow users to interrogate the same data and produce customised charts and other visualisation products.
Maintained by Ernest Guevarra. Last updated 1 months ago.
0.5 match 1 stars 2.00 scorecran
epade:Easy Plots
A collection of nice plotting functions directly from a data.frame with limited customisation possibilities.
Maintained by Andreas Schulz. Last updated 2 years ago.
0.6 match 1.60 scorecran
SPB:Simple Progress Bars for Procedural Coding
Provides a simple progress bar to use for basic and advanced users that suits all those who prefer procedural programming. It is especially useful for integration into markdown files thanks to the progress bar's customisable appearance.
Maintained by Fabio Ashtar Telarico. Last updated 3 years ago.
0.5 match 1.00 score
singator
autoharp:Semi-Automatic Grading of R and Rmd Scripts
A customisable set of tools for assessing and grading R or R-markdown scripts from students. It allows for checking correctness of code output, runtime statistics and static code analysis. The latter feature is made possible by representing R expressions using a tree structure.
Maintained by Vik Gopal. Last updated 3 years ago.
0.5 match 1 stars 1.00 score 8 scripts
florianpein
crossvalidationCP:Cross-Validation for Change-Point Regression
Implements the cross-validation methodology from Pein and Shah (2021) <arXiv:2112.03220>. Can be customised by providing different cross-validation criteria, estimators for the change-point locations and local parameters, and freely chosen folds. Pre-implemented estimators and criteria are available. It also includes our own implementation of the COPPS procedure <doi:10.1214/19-AOS1814>.
Maintained by Pein Florian. Last updated 2 years ago.
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9437951970
CompGR:Complete Annual Growth Rate Generator
It is designed to streamline the process of calculating complete annual growth rates with user-friendly functions and robust algorithms. It enables researchers and analysts to effortlessly generate precise growth rate estimates for their data. For method details see, Sharma, M.K.(2013) <https://www.indianjournals.com/ijor.aspx?target=ijor:jfl&volume=26&issue=1and2&article=018>. It offers a comprehensive suite of functions and customisable parameters. Equipped to handle varying complexities in data structures. It empowers users to uncover insightful growth dynamics and make informed decisions.
Maintained by Ashis Ranjan Udgata. Last updated 1 years ago.
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