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neuhausi

canvasXpress:Visualization Package for CanvasXpress in R

Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <https://www.canvasxpress.org> for more information.

Maintained by Connie Brett. Last updated 4 days ago.

analyticsbioinformaticschartchartingdashdashboarddata-analyticsdata-sciencedata-visualizationgenomicsgraphsjavascriptnetworknetwork-visualizationpythonreproducible-researchshinyvisualization

11.0 match 295 stars 11.39 score 145 scripts

bioc

EpiCompare:Comparison, Benchmarking & QC of Epigenomic Datasets

EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.

Maintained by Hiranyamaya Dash. Last updated 30 days ago.

epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsatacseqdnaseseqbenchmarkbenchmarkingbioconductorbioconductor-packagecomparisonhtmlinteractive-reporting

9.0 match 14 stars 7.54 score 46 scripts

alanarnholt

BSDA:Basic Statistics and Data Analysis

Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.

Maintained by Alan T. Arnholt. Last updated 2 years ago.

6.5 match 7 stars 9.11 score 1.3k scripts 6 dependents

bioc

MotifPeeker:Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo discovered motifs enriched in the datasets and compared with known motifs.

Maintained by Hiranyamaya Dash. Last updated 2 months ago.

epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsmotifdiscoverysequencematchingsoftwarealignmentbioconductorbioconductor-packagechip-seqepigenomicsinteractive-reportmotif-enrichment-analysis

9.0 match 2 stars 5.48 score 6 scripts

robinhankin

elliptic:Weierstrass and Jacobi Elliptic Functions

A suite of elliptic and related functions including Weierstrass and Jacobi forms. Also includes various tools for manipulating and visualizing complex functions.

Maintained by Robin K. S. Hankin. Last updated 12 days ago.

3.9 match 3 stars 9.31 score 54 scripts 79 dependents

r-lib

svglite:An 'SVG' Graphics Device

A graphics device for R that produces 'Scalable Vector Graphics'. 'svglite' is a fork of the older 'RSvgDevice' package.

Maintained by Thomas Lin Pedersen. Last updated 5 months ago.

svglibpngcpp

2.3 match 182 stars 15.51 score 4.7k scripts 223 dependents

r-lib

vdiffr:Visual Regression Testing and Graphical Diffing

An extension to the 'testthat' package that makes it easy to add graphical unit tests. It provides a Shiny application to manage the test cases.

Maintained by Lionel Henry. Last updated 5 months ago.

ggplot2graphicstestthatlibpngcpp

2.3 match 190 stars 10.77 score 254 scripts 5 dependents

dusadrian

admisc:Adrian Dusa's Miscellaneous

Contains functions used across packages 'DDIwR', 'QCA' and 'venn'. Interprets and translates, factorizes and negates SOP - Sum of Products expressions, for both binary and multi-value crisp sets, and extracts information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly versatile recoding routine and some more flexible alternatives to the base functions 'with()' and 'within()'. SOP simplification functions in this package use related minimization from package 'QCA', which is recommended to be installed despite not being listed in the Imports field, due to circular dependency issues.

Maintained by Adrian Dusa. Last updated 4 days ago.

3.0 match 2 stars 7.61 score 20 scripts 92 dependents

matthewheun

RCLabels:Manipulate Matrix Row and Column Labels with Ease

Functions to assist manipulation of matrix row and column labels for all types of matrix mathematics where row and column labels are to be respected.

Maintained by Matthew Heun. Last updated 11 days ago.

4.0 match 1 stars 4.78 score 5 scripts 2 dependents

noaa-nwfsc

zoid:Bayesian Zero-and-One Inflated Dirichlet Regression Modelling

Fits Dirichlet regression and zero-and-one inflated Dirichlet regression with Bayesian methods implemented in Stan. These models are sometimes referred to as trinomial mixture models; covariates and overdispersion can optionally be included.

Maintained by Eric J. Ward. Last updated 11 months ago.

mixture-modelsnwfsc-cbstancpp

3.1 match 8 stars 5.89 score 12 scripts

stscl

geocn:Loads Spatial Data Sets of China

Providing various commonly used spatial data related to Chinese regions in the R programming environment.

Maintained by Wenbo Lv. Last updated 3 months ago.

chinachina-regiongeospatial-visualizationmaps

3.4 match 17 stars 4.93 score 10 scripts

canmod

iidda:Processing Infectious Disease Datasets in IIDDA.

Part of an open toolchain for processing infectious disease datasets available through the IIDDA data repository.

Maintained by Steve Walker. Last updated 4 months ago.

1.8 match 6.07 score 133 scripts 3 dependents

bsnatr

tswge:Time Series for Data Science

Accompanies the texts Time Series for Data Science with R by Woodward, Sadler and Robertson & Applied Time Series Analysis with R, 2nd edition by Woodward, Gray, and Elliott. It is helpful for data analysis and for time series instruction.

Maintained by Bivin Sadler. Last updated 2 years ago.

3.2 match 2.70 score 496 scripts

hughparsonage

TeXCheckR:Parses LaTeX Documents for Errors

Checks LaTeX documents and .bib files for typing errors, such as spelling errors, incorrect quotation marks. Also provides useful functions for parsing and linting bibliography files.

Maintained by Hugh Parsonage. Last updated 1 years ago.

bibtexlatexspellcheck

1.9 match 8 stars 4.44 score 23 scripts

jrosell

jrrosell:Personal R package for Jordi Rosell

Useful functions for personal usage.

Maintained by Jordi Rosell. Last updated 3 months ago.

2.0 match 2 stars 3.08 score 7 scripts

daphnaharel

RPscoring:Relative Placement Algorithm

Implementation of the relative placement algorithm widely used in the scoring of Lindy Hop and West Coast Swing dance contests.

Maintained by Daphna Harel. Last updated 5 years ago.

2.3 match 2.00 score

forestscientist

StemAnalysis:Reconstructing Tree Growth and Carbon Accumulation with Stem Analysis Data

Use stem analysis data to reconstructing tree growth and carbon accumulation. Users can independently or in combination perform a number of standard tasks for any tree species. (i) Age class determination. (ii) The cumulative growth, mean annual increment, and current annual increment of diameter at breast height (DBH) with bark, tree height, and stem volume with bark are estimated. (iii) Tree biomass and carbon storage estimation from volume and allometric models are calculated. (iv) Height-diameter relationship is fitted with nonlinear models, if diameter at breast height (DBH) or tree height are available, which can be used to retrieve tree height and diameter at breast height (DBH). <https://github.com/forestscientist/StemAnalysis>.

Maintained by Huili Wu. Last updated 2 years ago.

1.0 match 4 stars 4.38 score 12 scripts

oldlipe

Rwtss:Client for Web Time-Series Service

Allows remote access to satellite image time series provided by the web time series service (WTSS) available at servers such as <https://brazildatacube.dpi.inpe.br/wtss/>. The functions include listing the data sets available in WTSS servers, describing the contents of a data set, and retrieving a time series based on spatial location and temporal filters.

Maintained by Felipe Souza. Last updated 3 years ago.

1.8 match 2.28 score 19 scripts

sahirbhatnagar

manhattanly:Interactive Q-Q and Manhattan Plots Using 'plotly.js'

Create interactive manhattan, Q-Q and volcano plots that are usable from the R console, in 'Dash' apps, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a point to show details or drag a rectangle to zoom. A manhattan plot is a popular graphical method for visualizing results from high-dimensional data analysis such as a (epi)genome wide association study (GWAS or EWAS), in which p-values, Z-scores, test statistics are plotted on a scatter plot against their genomic position. Manhattan plots are used for visualizing potential regions of interest in the genome that are associated with a phenotype. Interactive manhattan plots allow the inspection of specific value (e.g. rs number or gene name) by hovering the mouse over a cell, as well as zooming into a region of the genome (e.g. a chromosome) by dragging a rectangle around the relevant area. This work is based on the 'qqman' package and the 'plotly.js' engine. It produces similar manhattan and Q-Q plots as the 'manhattan' and 'qq' functions in the 'qqman' package, with the advantage of including extra annotation information and interactive web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.

Maintained by Sahir Bhatnagar. Last updated 4 years ago.

0.5 match 60 stars 7.15 score 78 scripts

cran

SSDforR:Functions to Analyze Single System Data

Functions to visually and statistically analyze single system data.

Maintained by Charles Auerbach. Last updated 4 hours ago.

1.9 match 1.62 score

doer0

doofa:Designs for Order-of-Addition Experiments

A facility to generate efficient designs for order-of-additions experiments under pair-wise-order model, see Dennis K. J. Lin and Jiayu Peng (2019)."Order-of-addition experiments: A review and some new thoughts". Quality Engineering, 31:1, 49-59, <doi:10.1080/08982112.2018.1548021>. It also provides a facility to generate component orthogonal arrays under component position model, see Jian-Feng Yang, Fasheng Sun & Hongquan Xu (2020): "A Component Position Model, Analysis and Design for Order-of-Addition Experiments". Technometrics, <doi:10.1080/00401706.2020.1764394>.

Maintained by Baidya Nath Mandal. Last updated 10 months ago.

1.6 match 1.48 score 1 dependents

doer0

ispd:Incomplete Split-Plot Designs

A collection of several functions related to construction and analysis of incomplete split-plot designs. The package contains functions to obtain and analyze incomplete split-plot designs for three kinds of situations namely (i) when blocks are complete with respect to main plot treatments and main plots are incomplete with respect to subplot treatments, (ii) when blocks are incomplete with respect to main plot treatments and main plots are complete with respect to subplot treatments and (iii) when blocks are incomplete with respect to main plot treatments and main plots are incomplete with respect to subplot treatments.

Maintained by Baidya Nath Mandal. Last updated 6 years ago.

1.6 match 1.00 score

doer0

Aoptbdtvc:A-Optimal Block Designs for Comparing Test Treatments with Controls

A collection of functions to construct A-optimal block designs for comparing test treatments with one or more control(s). Mainly A-optimal balanced treatment incomplete block designs, weighted A-optimal balanced treatment incomplete block designs, A-optimal group divisible treatment designs and A-optimal balanced bipartite block designs can be constructed using the package. The designs are constructed using algorithms based on linear integer programming. To the best of our knowledge, these facilities to construct A-optimal block designs for comparing test treatments with one or more controls are not available in the existing R packages. For more details on designs for tests versus control(s) comparisons, please see Hedayat, A. S. and Majumdar, D. (1984) <doi:10.1080/00401706.1984.10487989> A-Optimal Incomplete Block Designs for Control-Test Treatment Comparisons, Technometrics, 26, 363-370 and Mandal, B. N. , Gupta, V. K., Parsad, Rajender. (2017) <doi:10.1080/03610926.2015.1071394> Balanced treatment incomplete block designs through integer programming. Communications in Statistics - Theory and Methods 46(8), 3728-3737.

Maintained by Baidya Nath Mandal. Last updated 1 years ago.

1.6 match 1.00 score 3 scripts

doer0

pbbd:Position Balanced and Nearly Position Balanced Block Designs

Generates a position balanced or nearly position balanced block design with given parameters. This package can also convert a given proper and equireplicate block design into a position balanced or nearly position balanced block design.

Maintained by B N Mandal. Last updated 4 years ago.

1.6 match 1.00 score

doer0

slr:Semi-Latin Rectangles

A facility to generate balanced semi-Latin rectangles with any cell size (preferably up to ten) with given number of treatments, see Uto, N.P. and Bailey, R.A. (2020). "Balanced Semi-Latin rectangles: properties, existence and constructions for block size two". Journal of Statistical Theory and Practice, 14(3), 1-11, <doi:10.1007/s42519-020-00118-3>. It also provides facility to generate partially balanced semi-Latin rectangles for cell size 2, 3 and 4 for any number of treatments.

Maintained by Baidya Nath Mandal. Last updated 1 years ago.

1.6 match 1.00 score 2 scripts

doer0

mixOofA:Design and Analysis of Order-of-Addition Mixture Experiments

A facility to generate various classes of fractional designs for order-of-addition experiments namely fractional order-of-additions orthogonal arrays, see Voelkel, Joseph G. (2019). "The design of order-of-addition experiments." Journal of Quality Technology 51:3, 230-241, <doi:10.1080/00224065.2019.1569958>. Provides facility to construct component orthogonal arrays, see Jian-Feng Yang, Fasheng Sun and Hongquan Xu (2020). "A Component Position Model, Analysis and Design for Order-of-Addition Experiments." Technometrics, <doi:10.1080/00401706.2020.1764394>. Supports generation of fractional designs for order-of-addition mixture experiments. Analysis of data from order-of-addition mixture experiments is also supported.

Maintained by Baidya Nath Mandal. Last updated 8 months ago.

1.6 match 1.00 score

doer0

SlicedLHD:Sliced Latin Hypercube Designs

A facility to generate sliced (orthogonal) Latin hypercube designs with four and five slices. For details about sliced and orthogonal Latin hypercube designs, see Yang, J. F., Lin, C. D., Qian, P. Z., and Lin, D. K. (2013). "Construction of sliced orthogonal Latin hypercube designs". Statistica Sinica, 1117-1130, <doi:10.5705/ss.2012.037>.

Maintained by Baidya Nath Mandal. Last updated 1 years ago.

1.6 match 1.00 score

matt-dray

remorse:Translate Text to Morse to Sound

Converts a string input to Morse Code and back. Plays the Morse Code as audible dits and dahs (dots and dashes).

Maintained by Matt Dray. Last updated 2 years ago.

morse-code

0.5 match 3 stars 2.18 score

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