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r-gprofiler2
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public |
A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler/>). The main tools are: (1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists; (2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces; (3) 'g:Orth' - orthology search across species; (4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects. This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
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2024-01-16 |
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r-gptstudio
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public |
Large language models are readily accessible via API. This package lowers the barrier to use the API inside of your development environment. For more on the API, see <https://platform.openai.com/docs/introduction>.
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2024-01-16 |
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r-gpairs
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public |
Offers a generalization of the scatterplot matrix based on the recognition that most datasets include both categorical and quantitative information. Traditional grids of scatterplots often obscure important features of the data when one or more variables are categorical but coded as numerical. The generalized pairs plot offers a range of displays of paired combinations of categorical and quantitative variables. Emerson et al. (2013) <DOI:10.1080/10618600.2012.694762>.
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2024-01-16 |
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r-gradientpickerd3
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public |
Widget for an interactive selection and modification of a color gradient. 'gradientPickerD3' allows addition, removement and replacement of color ticks. List of numeric values will automatically translate in their corresponding tick position within the numeric range. App returns a data.frame containing tick values, colors and the positions in percent (0.0 to 1.0) for each color tick in the gradient. The original JS 'jquery-gradient-picker' was implemented by Matt Crinklaw-Vogt (nick: tantaman) <https://github.com/tantaman/>. Widget and JS modifications were done by CD. Peikert.
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2024-01-16 |
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r-grader
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public |
After being given the location of your students' submissions and a test file, the function runs each .R file, and evaluates the results from all the given tests. Results are neatly returned in a data frame that has a row for each student, and a column for each test.
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2024-01-16 |
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r-grade
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public |
Provides functions for matching student-answers to teacher answers for a variety of data types.
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2024-01-16 |
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r-gpfit
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public |
A computationally stable approach of fitting a Gaussian Process (GP) model to a deterministic simulator.
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2024-01-16 |
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r-gprofiler
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public |
This package has been deprecated and will not be updated. New users should use the package 'gprofiler2' (<https://CRAN.R-project.org/package=gprofiler2>) for up-to-date data and improved functionality. Functional enrichment analysis, gene identifier conversion and mapping homologous genes across related organisms via the 'g:Profiler' toolkit (<https://biit.cs.ut.ee/gprofiler/>).
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2024-01-16 |
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r-goplot
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public |
Implementation of multilayered visualizations for enhanced graphical representation of functional analysis data. It combines and integrates omics data derived from expression and functional annotation enrichment analyses. Its plotting functions have been developed with an hierarchical structure in mind: starting from a general overview to identify the most enriched categories (modified bar plot, bubble plot) to a more detailed one displaying different types of relevant information for the molecules in a given set of categories (circle plot, chord plot, cluster plot, Venn diagram, heatmap).
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2024-01-16 |
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r-gpltr
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public |
Combining a generalized linear model with an additional tree part on the same scale. A four-step procedure is proposed to fit the model and test the joint effect of the selected tree part while adjusting on confounding factors. We also proposed an ensemble procedure based on the bagging to improve prediction accuracy and computed several scores of importance for variable selection. See 'Cyprien Mbogning et al.'(2014)<doi:10.1186/2043-9113-4-6> and 'Cyprien Mbogning et al.'(2015)<doi:10.1159/000380850> for an overview of all the methods implemented in this package.
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2024-01-16 |
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r-gplots
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None |
Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary function as ('bandplot', 'wapply'), - enhanced versions of standard plots ('barplot2', 'boxplot2', 'heatmap.2', 'smartlegend'), - manipulating colors ('col2hex', 'colorpanel', 'redgreen', 'greenred', 'bluered', 'redblue', 'rich.colors'), - calculating and plotting two-dimensional data summaries ('ci2d', 'hist2d'), - enhanced regression diagnostic plots ('lmplot2', 'residplot'), - formula-enabled interface to 'stats::lowess' function ('lowess'), - displaying textual data in plots ('textplot', 'sinkplot'), - plotting a matrix where each cell contains a dot whose size reflects the relative magnitude of the elements ('balloonplot'), - plotting "Venn" diagrams ('venn'), - displaying Open-Office style plots ('ooplot'), - plotting multiple data on same region, with separate axes ('overplot'), - plotting means and confidence intervals ('plotCI', 'plotmeans'), - spacing points in an x-y plot so they don't overlap ('space').
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2024-01-16 |
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r-gpk
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public |
Collection of datasets as prepared by Profs. A.P. Gore, S.A. Paranjape, and M.B. Kulkarni of Department of Statistics, Poona University, India. With their permission, first letter of their names forms the name of this package, the package has been built by me and made available for the benefit of R users. This collection requires a rich class of models and can be a very useful building block for a beginner.
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2024-01-16 |
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r-gparotation
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public |
Gradient Projection Algorithms for Factor Rotation. For details see ?GPArotation. When using this package, please cite: Bernaards and Jennrich (2005) <doi:10.1177/0013164404272507>. "Gradient Projection Algorithms and Software for Arbitrary Rotation Criteria in Factor Analysis".
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2024-01-16 |
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r-govstatjpn
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public |
This package purposes to deal with public survey data of Japanese government via their Application Programming Interface (http://statdb.nstac.go.jp/)
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2024-01-16 |
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r-googleway
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public |
Provides a mechanism to plot a 'Google Map' from 'R' and overlay it with shapes and markers. Also provides access to 'Google Maps' APIs, including places, directions, roads, distances, geocoding, elevation and timezone.
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2024-01-16 |
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r-googlecomputeenginer
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public |
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.
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2024-01-16 |
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r-goric
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public |
Generalized Order-Restricted Information Criterion (GORIC) value for a set of hypotheses in multivariate linear models and generalised linear models.
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2024-01-16 |
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r-googlelanguager
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public |
Call 'Google Cloud' machine learning APIs for text and speech tasks. Call the 'Cloud Translation' API <https://cloud.google.com/translate/> for detection and translation of text, the 'Natural Language' API <https://cloud.google.com/natural-language/> to analyse text for sentiment, entities or syntax, the 'Cloud Speech' API <https://cloud.google.com/speech/> to transcribe sound files to text and the 'Cloud Text-to-Speech' API <https://cloud.google.com/text-to-speech/> to turn text into sound files.
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2024-01-16 |
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r-googlecloudstorager
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public |
Interact with Google Cloud Storage <https://cloud.google.com/storage/> API in R. Part of the 'cloudyr' <https://cloudyr.github.io/> project.
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2024-01-16 |
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r-googlevis
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public |
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.
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2024-01-16 |
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r-googlesheets4
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public |
Interact with Google Sheets through the Sheets API v4 <https://developers.google.com/sheets/api>. "API" is an acronym for "application programming interface"; the Sheets API allows users to interact with Google Sheets programmatically, instead of via a web browser. The "v4" refers to the fact that the Sheets API is currently at version 4. This package can read and write both the metadata and the cell data in a Sheet.
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2024-01-16 |
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r-googleauthr
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public |
Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility.
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2024-01-16 |
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r-googleknowledgegraphr
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public |
Allows you to retrieve information from the 'Google Knowledge Graph' API <https://www.google.com/intl/bn/insidesearch/features/search/knowledge.html> and process it in R in various forms. The 'Knowledge Graph Search' API lets you find entities in the 'Google Knowledge Graph'. The API uses standard 'schema.org' types and is compliant with the 'JSON-LD' specification.
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2024-01-16 |
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r-googledrive
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public |
Manage Google Drive files from R.
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2024-01-16 |
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r-googleanalyticsr
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public |
Interact with the Google Analytics APIs <https://developers.google.com/analytics/>, including the Core Reporting API (v3 and v4), Management API, User Activity API GA4's Data API and Admin API and Multi-Channel Funnel API.
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2024-01-16 |
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r-goodpractice
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public |
Give advice about good practices when building R packages. Advice includes functions and syntax to avoid, package structure, code complexity, code formatting, etc.
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2024-01-16 |
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r-golem
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public |
An opinionated framework for building a production-ready 'Shiny' application. This package contains a series of tools for building a robust 'Shiny' application from start to finish.
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2024-01-16 |
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r-goeveg
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public |
A collection of functions useful in (vegetation) community analyses and ordinations. Includes automatic species selection for ordination diagrams, NMDS stress/scree plots, species response curves and rank-abundance curves as well as calculation and sorting of synoptic tables.
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2024-01-16 |
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r-goodmankruskal
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public |
Association analysis between categorical variables using the Goodman and Kruskal tau measure. This asymmetric association measure allows the detection of asymmetric relations between categorical variables (e.g., one variable obtained by re-grouping another).
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2024-01-16 |
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r-gomms
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public |
A zero-inflated quasi-Poisson factor model to display similarity between samples visually in a low (2 or 3) dimensional space.
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2024-01-16 |
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r-gogarch
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public |
Provision of classes and methods for estimating generalized orthogonal GARCH models. This is an alternative approach to CC-GARCH models in the context of multivariate volatility modeling.
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2024-01-16 |
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r-gmoip
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public |
Make 2D and 3D plots of linear programming (LP), integer linear programming (ILP), or mixed integer linear programming (MILP) models with up to three objectives. Plots of both the solution and criterion space are possible. For instance the non-dominated (Pareto) set for bi-objective LP/ILP/MILP programming models (see vignettes for an overview). The package also contains an function for checking if a point is inside the convex hull.
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2024-01-16 |
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r-gnorm
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public |
Functions for obtaining generalized normal/exponential power distribution probabilities, quantiles, densities and random deviates. The generalized normal/exponential power distribution was introduced by Subbotin (1923) and rediscovered by Nadarajah (2005). The parametrization given by Nadarajah (2005) <doi:10.1080/02664760500079464> is used.
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2024-01-16 |
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r-gofkernel
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public |
Tests of goodness-of-fit based on a kernel smoothing of the data.
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2024-01-16 |
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r-gmnl
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public |
An implementation of maximum simulated likelihood method for the estimation of multinomial logit models with random coefficients as presented by Sarrias and Daziano (2017) <doi:10.18637/jss.v079.i02>. Specifically, it allows estimating models with continuous heterogeneity such as the mixed multinomial logit and the generalized multinomial logit. It also allows estimating models with discrete heterogeneity such as the latent class and the mixed-mixed multinomial logit model.
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2024-01-16 |
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r-gnumeric
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public |
Read data files readable by 'gnumeric' into 'R'. Can read whole sheet or a range, from several file formats, including the native format of 'gnumeric'. Reading is done by using 'ssconvert' (a file converter utility included in the 'gnumeric' distribution <http://www.gnumeric.org>) to convert the requested part to CSV. From 'gnumeric' files (but not other formats) can list sheet names and sheet sizes or read all sheets.
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2024-01-16 |
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r-gmt
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public |
Interface between the GMT map-making software and R, enabling the user to manipulate geographic data within R and call GMT commands to draw and annotate maps in postscript format. The gmt package is about interactive data analysis, rapidly visualizing subsets and summaries of geographic data, while performing statistical analysis in the R console.
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2024-01-16 |
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r-gmailr
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public |
An interface to the 'Gmail' 'RESTful' API. Allows access to your 'Gmail' messages, threads, drafts and labels.
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2024-01-16 |
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r-gmodels
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public |
Various R programming tools for model fitting.
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2024-01-16 |
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r-glmpca
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public |
Implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed data such as counts or binary matrices. Townes FW, Hicks SC, Aryee MJ, Irizarry RA (2019) <doi:10.1186/s13059-019-1861-6>. Townes FW (2019) <arXiv:1907.02647>.
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2024-01-16 |
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r-gmmboost
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public |
Likelihood-based boosting approaches for generalized mixed models are provided.
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2024-01-16 |
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r-gmfd
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public |
Some methods for the inference and clustering of univariate and multivariate functional data, using a generalization of Mahalanobis distance, along with some functions useful for the analysis of functional data. For further details, see Martino A., Ghiglietti, A., Ieva, F. and Paganoni A. M. (2017) <arXiv:1708.00386>.
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2024-01-16 |
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r-gmdhreg
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public |
Regression using GMDH algorithms from Prof. Alexey G. Ivakhnenko. Group Method of Data Handling (GMDH), or polynomial neural networks, is a family of inductive algorithms that performs gradually complicated polynomial models and selecting the best solution by an external criterion. In other words, inductive GMDH algorithms give possibility finding automatically interrelations in data, and selecting an optimal structure of model or network. The package includes GMDH Combinatorial, GMDH MIA (Multilayered Iterative Algorithm), GMDH GIA (Generalized Iterative Algorithm) and GMDH Combinatorial with Active Neurons.
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2024-01-16 |
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r-gmdh
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public |
Group method of data handling (GMDH) - type neural network algorithm is the heuristic self-organization method for modelling the complex systems. In this package, GMDH-type neural network algorithms are applied to make short term forecasting for a univariate time series.
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2024-01-16 |
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r-glmtoolbox
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public |
Set of tools to the statistical analysis of data using: (1) normal linear models; (2) generalized linear models; (3) negative binomial regression models as alternative to the Poisson regression models under the presence of overdispersion; (4) beta-binomial and random-clumped binomial regression models as alternative to the binomial regression models under the presence of overdispersion; (5) Zero-inflated and zero-altered regression models to deal with zero-excess in count data; (6) generalized estimating equations for cluster correlated data.
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2024-01-16 |
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r-gmdatabase
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public |
A template for a geometallurgical database and a fast and easy interface for accessing it is provided in this package.
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2024-01-16 |
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r-gmapsdistance
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public |
Get distance and travel time between two points from Google Maps. Four possible modes of transportation (bicycling, walking, driving and public transportation).
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2024-01-16 |
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r-gmac
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public |
Performs genomic mediation analysis with adaptive confounding adjustment (GMAC) proposed by Yang et al. (2017) <doi:10.1101/078683>. It implements large scale mediation analysis and adaptively selects potential confounding variables to adjust for each mediation test from a pool of candidate confounders. The package is tailored for but not limited to genomic mediation analysis (e.g., cis-gene mediating trans-gene regulation pattern where an eQTL, its cis-linking gene transcript, and its trans-gene transcript play the roles as treatment, mediator and the outcome, respectively), restricting to scenarios with the presence of cis-association (i.e., treatment-mediator association) and random eQTL (i.e., treatment).
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2024-01-16 |
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r-glsme
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public |
Performs linear regression with correlated predictors, responses and correlated measurement errors in predictors and responses, correcting for biased caused by these.
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2024-01-16 |
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r-glrth
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public |
Likelihood ratio tests for genome-wide association and genome-wide linkage analysis under heterogeneity.
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2024-01-16 |
