R-universe search: needs:ggfittext

wilkox

treemapify:Draw Treemaps in 'ggplot2'

Provides 'ggplot2' geoms for drawing treemaps.

Maintained by David Wilkins. Last updated 10 months ago.

data-visualisation ggplot2 treemap

215 stars 12.58 score 1.6k scripts 9 dependents

wilkox

gggenes:Draw Gene Arrow Maps in 'ggplot2'

A 'ggplot2' extension for drawing gene arrow maps.

Maintained by David Wilkins. Last updated 2 years ago.

genetics ggplot2

527 stars 10.69 score 372 scripts 2 dependents

willgearty

deeptime:Plotting Tools for Anyone Working in Deep Time

Extends the functionality of other plotting packages (notably 'ggplot2') to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of 'deeptime' is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.

Maintained by William Gearty. Last updated 3 months ago.

geology ggplot2 paleontology visualization

92 stars 10.46 score 207 scripts 3 dependents

modeloriented

shapviz:SHAP Visualizations

Visualizations for SHAP (SHapley Additive exPlanations), such as waterfall plots, force plots, various types of importance plots, dependence plots, and interaction plots. These plots act on a 'shapviz' object created from a matrix of SHAP values and a corresponding feature dataset. Wrappers for the R packages 'xgboost', 'lightgbm', 'fastshap', 'shapr', 'h2o', 'treeshap', 'DALEX', and 'kernelshap' are added for convenience. By separating visualization and computation, it is possible to display factor variables in graphs, even if the SHAP values are calculated by a model that requires numerical features. The plots are inspired by those provided by the 'shap' package in Python, but there is no dependency on it.

Maintained by Michael Mayer. Last updated 2 months ago.

explainable-ai machine-learning shap shapley-value visualization xai

90 stars 10.07 score 250 scripts

grunwaldlab

metacoder:Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) <doi:10.1371/journal.pcbi.1005404>.

Maintained by Zachary Foster. Last updated 2 months ago.

community-diversity hierarchical metabarcoding pcr taxonomy trees cpp

140 stars 9.64 score 328 scripts

sportsdataverse

sportyR:Plot Scaled 'ggplot' Representations of Sports Playing Surfaces

Create scaled 'ggplot' representations of playing surfaces. Playing surfaces are drawn pursuant to rule-book specifications. This package should be used as a baseline plot for displaying any type of tracking data.

Maintained by Ross Drucker. Last updated 2 months ago.

football ggplot2 playing-surfaces sport sports-analytics sports-data sports-tracking-data sportsdataverse visualization

104 stars 8.08 score 97 scripts

alastairrushworth

inspectdf:Inspection, Comparison and Visualisation of Data Frames

A collection of utilities for columnwise summary, comparison and visualisation of data frames. Functions report missingness, categorical levels, numeric distribution, correlation, column types and memory usage.

Maintained by Alastair Rushworth. Last updated 3 years ago.

comparison dataframe eda exploratory-data-analysis visualization cpp

251 stars 7.77 score 444 scripts 1 dependents

epiverse-trace

epiCo:Statistical and Viz Tools for Vector-Borne Diseases in Colombia

Provides statistical and visualization tools for the analysis of demographic indicators, and spatio-temporal behavior and characterization of outbreaks of vector-borne diseases (VBDs) in Colombia. It implements travel times estimated in Bravo-Vega C., Santos-Vega M., & Cordovez J.M. (2022), and the endemic channel method (Bortman, M. (1999) <https://iris.paho.org/handle/10665.2/8562>).

Maintained by Juan D. Umaña. Last updated 3 months ago.

colombia decision-support demographics epiverse outbreak-analysis sdg-3 spatio-temporal-analysis vector-borne-diseases

12 stars 6.94 score 8 scripts

rsquaredacademy

rfm:Recency, Frequency and Monetary Value Analysis

Tools for RFM (recency, frequency and monetary value) analysis. Generate RFM score from both transaction and customer level data. Visualize the relationship between recency, frequency and monetary value using heatmap, histograms, bar charts and scatter plots. Includes a 'shiny' app for interactive segmentation. References: i. Blattberg R.C., Kim BD., Neslin S.A (2008) <doi:10.1007/978-0-387-72579-6_12>.

Maintained by Aravind Hebbali. Last updated 1 years ago.

customer-analytics customer-segmentation rfm-analysis segmentation

61 stars 6.68 score 94 scripts

loukiaspin

rnmamod:Bayesian Network Meta-Analysis with Missing Participants

A comprehensive suite of functions to perform and visualise pairwise and network meta-analysis with aggregate binary or continuous missing participant outcome data. The package covers core Bayesian one-stage models implemented in a systematic review with multiple interventions, including fixed-effect and random-effects network meta-analysis, meta-regression, evaluation of the consistency assumption via the node-splitting approach and the unrelated mean effects model (original and revised model proposed by Spineli, (2022) <doi:10.1177/0272989X211068005>), and sensitivity analysis (see Spineli et al., (2021) <doi:10.1186/s12916-021-02195-y>). Missing participant outcome data are addressed in all models of the package (see Spineli, (2019) <doi:10.1186/s12874-019-0731-y>, Spineli et al., (2019) <doi:10.1002/sim.8207>, Spineli, (2019) <doi:10.1016/j.jclinepi.2018.09.002>, and Spineli et al., (2021) <doi:10.1002/jrsm.1478>). The robustness to primary analysis results can also be investigated using a novel intuitive index (see Spineli et al., (2021) <doi:10.1177/0962280220983544>). Methods to evaluate the transitivity assumption quantitatively are provided (see Spineli, (2024) <doi:10.1186/s12874-024-02436-7>). A novel index to facilitate interpretation of local inconsistency is also available (see Spineli, (2024) <doi:0.1186/s13643-024-02680-4>) The package also offers a rich, user-friendly visualisation toolkit that aids in appraising and interpreting the results thoroughly and preparing the manuscript for journal submission. The visualisation tools comprise the network plot, forest plots, panel of diagnostic plots, heatmaps on the extent of missing participant outcome data in the network, league heatmaps on estimation and prediction, rankograms, Bland-Altman plot, leverage plot, deviance scatterplot, heatmap of robustness, barplot of Kullback-Leibler divergence, heatmap of comparison dissimilarities and dendrogram of comparison clustering. The package also allows the user to export the results to an Excel file at the working directory.

Maintained by Loukia Spineli. Last updated 26 days ago.

jags cpp

5 stars 6.64 score 12 scripts

dmenne

breathtestcore:Core Functions to Read and Fit 13c Time Series from Breath Tests

Reads several formats of 13C data (IRIS/Wagner, BreathID) and CSV. Creates artificial sample data for testing. Fits Maes/Ghoos, Bluck-Coward self-correcting formula using 'nls', 'nlme'. Methods to fit breath test curves with Bayesian Stan methods are refactored to package 'breathteststan'. For a Shiny GUI, see package 'dmenne/breathtestshiny' on github.

Maintained by Dieter Menne. Last updated 3 months ago.

13c breath breath-test gastroenterology medical stan

2 stars 6.19 score 64 scripts 1 dependents

revbayes

RevGadgets:Visualization and Post-Processing of 'RevBayes' Analyses

Processes and visualizes the output of complex phylogenetic analyses from the 'RevBayes' phylogenetic graphical modeling software.

Maintained by Carrie Tribble. Last updated 1 years ago.

13 stars 6.09 score 208 scripts

gbganalyst

bulkreadr:The Ultimate Tool for Reading Data in Bulk

Designed to simplify and streamline the process of reading and processing large volumes of data in R, this package offers a collection of functions tailored for bulk data operations. It enables users to efficiently read multiple sheets from Microsoft Excel and Google Sheets workbooks, as well as various CSV files from a directory. The data is returned as organized data frames, facilitating further analysis and manipulation. Ideal for handling extensive data sets or batch processing tasks, bulkreadr empowers users to manage data in bulk effortlessly, saving time and effort in data preparation workflows. Additionally, the package seamlessly works with labelled data from SPSS and Stata.

Maintained by Ezekiel Ogundepo. Last updated 7 months ago.

bulkreader csv-reader data-import googlesheets missing-values xlsxreader

12 stars 5.94 score 12 scripts

ropensci

phylotaR:Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.

Maintained by Shixiang Wang. Last updated 9 months ago.

blastn genbank peer-reviewed phylogenetics sequence-alignment

23 stars 5.86 score 156 scripts

bioc

ChromSCape:Analysis of single-cell epigenomics datasets with a Shiny App

ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.

Maintained by Pacome Prompsy. Last updated 5 months ago.

shinyapps software singlecell chipseq atacseq methylseq classification clustering epigenetics principalcomponent annotation batcheffect multiplecomparison normalization pathways preprocessing qualitycontrol reportwriting visualization genesetenrichment differentialpeakcalling epigenomics shiny single-cell cpp

14 stars 5.83 score 16 scripts

tiago-simoes

EvoPhylo:Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

Performs automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses, following concepts introduced by Simões and Pierce (2021) <doi:10.1038/s41559-021-01532-x>.

Maintained by Tiago Simoes. Last updated 2 years ago.

4 stars 5.66 score 19 scripts

mums2

mpactr:Correction of Preprocessed MS Data

An 'R' implementation of the 'python' program Metabolomics Peak Analysis Computational Tool ('MPACT') (Robert M. Samples, Sara P. Puckett, and Marcy J. Balunas (2023) <doi:10.1021/acs.analchem.2c04632>). Filters in the package serve to address common errors in tandem mass spectrometry preprocessing, including: (1) isotopic patterns that are incorrectly split during preprocessing, (2) features present in solvent blanks due to carryover between samples, (3) features whose abundance is greater than user-defined abundance threshold in a specific group of samples, for example media blanks, (4) ions that are inconsistent between technical replicates, and (5) in-source fragment ions created during ionization before fragmentation in the tandem mass spectrometry workflow.

Maintained by Patrick Schloss. Last updated 5 days ago.

cpp

1 stars 5.59 score 4 scripts

bioc

ribosomeProfilingQC:Ribosome Profiling Quality Control

Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.

Maintained by Jianhong Ou. Last updated 2 months ago.

riboseq sequencing generegulation qualitycontrol visualization coverage

4.88 score 17 scripts

anthonypileggi

worrrd:Generate Wordsearch and Crossword Puzzles

Generate wordsearch and crossword puzzles using custom lists of words (and clues). Make them easy or hard, and print them to solve offline with paper and pencil!

Maintained by Anthony Pileggi. Last updated 2 years ago.

7 stars 4.66 score 13 scripts

cortinah

hockeystick:Download and Visualize Essential Climate Change Data

Provides easy access to essential climate change datasets to non-climate experts. Users can download the latest raw data from authoritative sources and view it via pre-defined 'ggplot2' charts. Datasets include atmospheric CO2, methane, emissions, instrumental and proxy temperature records, sea levels, Arctic/Antarctic sea-ice, Hurricanes, and Paleoclimate data. Sources include: NOAA Mauna Loa Laboratory <https://gml.noaa.gov/ccgg/trends/data.html>, Global Carbon Project <https://www.globalcarbonproject.org/carbonbudget/>, NASA GISTEMP <https://data.giss.nasa.gov/gistemp/>, National Snow and Sea Ice Data Center <https://nsidc.org/home>, CSIRO <https://research.csiro.au/slrwavescoast/sea-level/measurements-and-data/sea-level-data/>, NOAA Laboratory for Satellite Altimetry <https://www.star.nesdis.noaa.gov/socd/lsa/SeaLevelRise/> and HURDAT Atlantic Hurricane Database <https://www.aoml.noaa.gov/hrd/hurdat/Data_Storm.html>, Vostok Paleo carbon dioxide and temperature data: <doi:10.3334/CDIAC/ATG.009>.

Maintained by Hernando Cortina. Last updated 4 months ago.

carbon carbon-dioxide-data carbon-emissions climate climate-change climate-data climate-science ggplot2 methane noaa sea-ice sea-levels temperature-data warming-stripes

50 stars 4.40 score 8 scripts

dmenne

breathteststan:Stan-Based Fit to Gastric Emptying Curves

Stan-based curve-fitting function for use with package 'breathtestcore' by the same author. Stan functions are refactored here for easier testing.

Maintained by Dieter Menne. Last updated 3 months ago.

bayesian-methods fitting medical nonlinear stan cpp

3 stars 4.18 score 9 scripts

lilleoel

clintools:Tools for Clinical Research

Every research team have their own script for data management, statistics and most importantly hemodynamic indices. The purpose is to standardize scripts utilized in clinical research. The hemodynamic indices can be used in a long-format dataframe, and add both periods of interest (trigger-periods), and delete artifacts with deleter-files. Transfer function analysis (Claassen et al. (2016) <doi:10.1177/0271678X15626425>) and Mx (Czosnyka et al. (1996) <doi:10.1161/01.str.27.10.1829>) can be calculated using this package.

Maintained by Markus Harboe Olsen. Last updated 5 days ago.

2 stars 3.85 score

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.

83 stars 3.62 score 6 scripts

fmmattioni

metabolic:Datasets and Functions for Reproducing Meta-Analyses

Dataset and functions from the meta-analysis published in Medicine & Science in Sports & Exercise. It contains all the data and functions to reproduce the analysis. "Effectiveness of HIIE versus MICT in Improving Cardiometabolic Risk Factors in Health and Disease: A Meta-analysis". Felipe Mattioni Maturana, Peter Martus, Stephan Zipfel, Andreas M Nieß (2020) <doi:10.1249/MSS.0000000000002506>.

Maintained by Felipe Mattioni Maturana. Last updated 1 years ago.

8 stars 3.60 score 8 scripts

mladenjovanovic

STMr:Strength Training Manual R-Language Functions

Strength training prescription using percent-based approach requires numerous computations and assumptions. 'STMr' package allow users to estimate individual reps-max relationships, implement various progression tables, and create numerous set and rep schemes. The 'STMr' package is originally created as a tool to help writing Jovanović M. (2020) Strength Training Manual <ISBN:979-8604459898>.

Maintained by Mladen Jovanović. Last updated 1 years ago.

5 stars 3.40 score 3 scripts

lewisajones

sepkoski:Sepkoski's Fossil Marine Animal Genera Compendium

Stratigraphic ranges of fossil marine animal genera from Sepkoski's (2002) published compendium. No changes have been made to any taxonomic names. However, first and last appearance intervals have been updated to be consistent with stages of the International Geological Timescale. Functionality for generating a plot of Sepkoski's evolutionary fauna is also included. For specific details on the compendium see: Sepkoski, J. J. (2002). A compendium of fossil marine animal genera. Bulletins of American Paleontology, 363, pp. 1–560 (ISBN 0-87710-450-6). Access: <https://www.biodiversitylibrary.org/item/40634#page/5/mode/1up>.

Maintained by Lewis A. Jones. Last updated 6 months ago.

2 stars 3.30 score 3 scripts

coreofscience

margaret:Scientometric Analysis Minciencias

The target of 'margaret' is help to extract data from Minciencias to analyze scientific production in Colombia.

Maintained by Bryan Arias. Last updated 2 years ago.

3 stars 3.18 score 4 scripts

teachinglab

tlShiny:Supplies essential functions to Teaching Lab dashboards

A bunch of random functions I use in developing dashboards Needs to vastly reduce the number of dependencies at the moment.

Maintained by Duncan Gates. Last updated 6 days ago.

3.04 score

adafede

sapid:A Strategy to Analyze Plant Extracts Taste In Depth

This package provides the infrastructure to implement a Strategy to Analyze Plant Extracts Taste In Depth.

Maintained by Adriano Rutz. Last updated 8 hours ago.

computationalmetabolomics naturalextracts taste

2.93 score

c7rishi

pvLRT:Likelihood Ratio Test-Based Approaches to Pharmacovigilance

A suite of likelihood ratio test based methods to use in pharmacovigilance. Contains various testing and post-processing functions.

Maintained by Saptarshi Chakraborty. Last updated 2 years ago.

1 stars 2.70 score 9 scripts

pr2database

metapr2:Eukaryotic 18S rRNA metabarcode database

Provides an interface to the metaPR2 database (current version = 1.0) which contains eukaryotic 18S rRNA metabarcodes. Many options for selecting samples are provided. Data can be displayed as maps, barplots, treemaps. Data can be searched and downloaded. See https://pr2-database.org for more information.

Maintained by Daniel Vaulot. Last updated 1 years ago.

18s-rrna metabarcoding shiny-apps

3 stars 2.18 score

cran

time.slots:Display Data in a Weekly Calendar View

Generate weekly timetables as a ggplot2 layer. Add informative timeslots with elements such as title, key-value pairs, or colour to reveal trends.

Maintained by Mukti Rathod. Last updated 3 years ago.

1.70 score

cran

plothelper:New Plots Based on 'ggplot2' and Functions to Create Regular Shapes

An extension to 'ggplot2' and 'magick'. It contains three groups of functions: Functions in the first group draw 'ggplot2' - based plots: geom_shading_bar() draws barplot with shading colors in each bar. geom_rect_cm(), geom_circle_cm() and geom_ellipse_cm() draw rectangles, circles and ellipses with centimeter as their unit. Thus their sizes do not change when the coordinate system or the aspect ratio changes. annotation_transparent_text() draws labels with transparent texts. annotation_shading_polygon() draws irregular polygons with shading colors. Functions in the second group generate coordinates for regular shapes and make linear transformations. Functions in the third group are 'magick' - based functions facilitating image processing.

Maintained by Jiang Wu. Last updated 5 years ago.

1.00 score