Showing 31 of total 31 results (show query)
tidyverse
tibble:Simple Data Frames
Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the traditional data frame.
Maintained by Kirill Müller. Last updated 9 days ago.
693 stars 22.85 score 47k scripts 11k dependents
dcomtois
summarytools:Tools to Quickly and Neatly Summarize Data
Data frame summaries, cross-tabulations, weight-enabled frequency tables and common descriptive (univariate) statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.
Maintained by Dominic Comtois. Last updated 3 days ago.
descriptive-statisticsfrequency-tablehtml-reportmarkdownpanderpandocpandoc-markdownrmarkdownrstudio
527 stars 14.62 score 2.9k scripts 6 dependents
melff
memisc:Management of Survey Data and Presentation of Analysis Results
An infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) 'SPSS' and 'Stata' files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to 'LaTeX' and HTML.
Maintained by Martin Elff. Last updated 24 days ago.
46 stars 12.34 score 1.2k scripts 13 dependents
bioc
ShortRead:FASTQ input and manipulation
This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
8 stars 12.08 score 1.8k scripts 49 dependents
christophsax
seasonal:R Interface to X-13-ARIMA-SEATS
Easy-to-use interface to X-13-ARIMA-SEATS, the seasonal adjustment software by the US Census Bureau. It offers full access to almost all options and outputs of X-13, including X-11 and SEATS, automatic ARIMA model search, outlier detection and support for user defined holiday variables, such as Chinese New Year or Indian Diwali. A graphical user interface can be used through the 'seasonalview' package. Uses the X-13-binaries from the 'x13binary' package.
Maintained by Christoph Sax. Last updated 28 days ago.
seasonal-adjustmenttime-series
120 stars 12.03 score 1.1k scripts 8 dependents
winvector
wrapr:Wrap R Tools for Debugging and Parametric Programming
Tools for writing and debugging R code. Provides: '%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to (R style multiple assignment/return), 'build_frame()'/'draw_frame()' ('data.frame' example tools), 'qc()' (quoting concatenate), ':=' (named map builder), 'let()' (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools::strmacro()' and 'base::bquote()'), and more.
Maintained by John Mount. Last updated 2 years ago.
137 stars 11.11 score 390 scripts 12 dependents
r-lum
Luminescence:Comprehensive Luminescence Dating Data Analysis
A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Maintained by Sebastian Kreutzer. Last updated 13 hours ago.
bayesian-statisticsdata-sciencegeochronologyluminescenceluminescence-datingopen-scienceoslplottingradiofluorescencetlxsygcpp
15 stars 10.66 score 178 scripts 8 dependents
jonclayden
RNifti:Fast R and C++ Access to NIfTI Images
Provides very fast read and write access to images stored in the NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation of in-memory image objects between compiled C and interpreted R code. Also provides a simple image viewer, and a C/C++ API that can be used by other packages. Not to be confused with 'RNiftyReg', which performs image registration and applies spatial transformations.
Maintained by Jon Clayden. Last updated 1 months ago.
medical-imagingnifti-formatzlibcpp
49 stars 10.48 score 522 scripts 56 dependentsbioc
ChemmineR:Cheminformatics Toolkit for R
ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.
Maintained by Thomas Girke. Last updated 5 months ago.
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp
15 stars 10.45 score 253 scripts 12 dependents
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 24 days ago.
3 stars 9.31 score 54 scripts 79 dependents
schaffman5
rtf:Rich Text Format (RTF) Output
A set of R functions to output Rich Text Format (RTF) files with high resolution tables and graphics that may be edited with a standard word processor such as Microsoft Word.
Maintained by Michael E. Schaffer. Last updated 6 years ago.
5 stars 8.59 score 169 scripts 10 dependentsbioc
TRONCO:TRONCO, an R package for TRanslational ONCOlogy
The TRONCO (TRanslational ONCOlogy) R package collects algorithms to infer progression models via the approach of Suppes-Bayes Causal Network, both from an ensemble of tumors (cross-sectional samples) and within an individual patient (multi-region or single-cell samples). The package provides parallel implementation of algorithms that process binary matrices where each row represents a tumor sample and each column a single-nucleotide or a structural variant driving the progression; a 0/1 value models the absence/presence of that alteration in the sample. The tool can import data from plain, MAF or GISTIC format files, and can fetch it from the cBioPortal for cancer genomics. Functions for data manipulation and visualization are provided, as well as functions to import/export such data to other bioinformatics tools for, e.g, clustering or detection of mutually exclusive alterations. Inferred models can be visualized and tested for their confidence via bootstrap and cross-validation. TRONCO is used for the implementation of the Pipeline for Cancer Inference (PICNIC).
Maintained by Luca De Sano. Last updated 2 days ago.
biomedicalinformaticsbayesiangraphandnetworksomaticmutationnetworkinferencenetworkclusteringdataimportsinglecellimmunooncologyalgorithmscancer-inferencetumors
30 stars 8.35 score 38 scripts
henrikbengtsson
R.rsp:Dynamic Generation of Scientific Reports
The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
documentmarkupreportreproducibilityscience
31 stars 8.06 score 36 scripts 9 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.
21 stars 8.06 score 362 scripts
polmine
polmineR:Verbs and Nouns for Corpus Analysis
Package for corpus analysis using the Corpus Workbench ('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create subcorpora and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document-term matrices, term-co-occurrence matrices etc.) can be created based on the indexed corpora.
Maintained by Andreas Blaette. Last updated 1 years ago.
49 stars 7.96 score 311 scriptsbioc
ropls:PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
Latent variable modeling with Principal Component Analysis (PCA) and Partial Least Squares (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial Least Squares (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. Successful applications of these chemometrics techniques include spectroscopic data such as Raman spectroscopy, nuclear magnetic resonance (NMR), mass spectrometry (MS) in metabolomics and proteomics, but also transcriptomics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients). The package can be accessed via a user interface on the Workflow4Metabolomics.org online resource for computational metabolomics (built upon the Galaxy environment).
Maintained by Etienne A. Thevenot. Last updated 5 months ago.
regressionclassificationprincipalcomponenttranscriptomicsproteomicsmetabolomicslipidomicsmassspectrometryimmunooncology
7.55 score 210 scripts 8 dependents
pbs-software
PBSmodelling:GUI Tools Made Easy: Interact with Models and Explore Data
Provides software to facilitate the design, testing, and operation of computer models. It focuses particularly on tools that make it easy to construct and edit a customized graphical user interface ('GUI'). Although our simplified 'GUI' language depends heavily on the R interface to the 'Tcl/Tk' package, a user does not need to know 'Tcl/Tk'. Examples illustrate models built with other R packages, including 'PBSmapping', 'PBSddesolve', and 'BRugs'. A complete user's guide 'PBSmodelling-UG.pdf' shows how to use this package effectively.
Maintained by Rowan Haigh. Last updated 5 months ago.
2 stars 6.76 score 120 scripts 4 dependents
fvafrcu
fritools:Utilities for the Forest Research Institute of the State Baden-Wuerttemberg
Miscellaneous utilities, tools and helper functions for finding and searching files on disk, searching for and removing R objects from the workspace. Does not import or depend on any third party package, but on core R only (i.e. it may depend on packages with priority 'base').
Maintained by Andreas Dominik Cullmann. Last updated 1 months ago.
5.82 score 4 scripts 6 dependentschristophsax
seasonalview:Graphical User Interface for Seasonal Adjustment
A graphical user interface to the 'seasonal' package and 'X-13ARIMA-SEATS', the U.S. Census Bureau's seasonal adjustment software.
Maintained by Christoph Sax. Last updated 5 months ago.
seasonal-adjustmentshinytime-series
22 stars 5.65 score 105 scriptsbioc
rCGH:Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.
Maintained by Frederic Commo. Last updated 5 months ago.
acghcopynumbervariationpreprocessingfeatureextraction
4 stars 5.10 score 26 scripts 1 dependents
r-lidar
lidRviewer:3D point cloud viewer
An advanced point cloud viewer designed to fluidly display hundreds of millions of points while using minimal memory. This package is intended as a replacement for rgl in lidR when the point cloud size exceeds what rgl can handle.
Maintained by Jean-Romain Roussel. Last updated 3 months ago.
84 stars 4.83 score 7 scripts
cfhammill
lenses:Elegant Data Manipulation with Lenses
Provides tools for creating and using lenses to simplify data manipulation. Lenses are composable getter/setter pairs for working with data in a purely functional way. Inspired by the 'Haskell' library 'lens' (Kmett, 2012) <https://hackage.haskell.org/package/lens>. For a fairly comprehensive (and highly technical) history of lenses please see the 'lens' wiki <https://github.com/ekmett/lens/wiki/History-of-Lenses>.
Maintained by Chris Hammill. Last updated 6 years ago.
27 stars 4.75 score 42 scripts
hanase
vote:Election Vote Counting
Counting election votes and determining election results by different methods, including the single transferable vote or ranked choice, approval, score, plurality, condorcet and two-round runoff methods (Raftery et al., 2021 <doi:10.32614/RJ-2021-086>).
Maintained by Hana Sevcikova. Last updated 26 days ago.
4 stars 4.38 score 30 scripts
arbelt
tinylens:Minimal Implementation of Functional Lenses
Provides utilities to create and use lenses to simplify data manipulation. Lenses are composable getter/setter pairs that provide a functional approach to manipulating deeply nested data structures, e.g., elements within list columns in data frames. The implementation is based on the earlier 'lenses' R package <https://github.com/cfhammill/lenses>, which was inspired by the Haskell 'lens' package by Kmett (2012) <https://github.com/ekmett/lens>, one of the most widely referenced implementations of lenses. For additional background and history on the theory of lenses, see the 'lens' package wiki: <https://github.com/ekmett/lens/wiki/History-of-Lenses>.
Maintained by Albert Wang. Last updated 4 months ago.
2 stars 3.70 score 3 scripts
jgarriga65
EMbC:Expectation-Maximization Binary Clustering
Unsupervised, multivariate, binary clustering for meaningful annotation of data, taking into account the uncertainty in the data. A specific constructor for trajectory analysis in movement ecology yields behavioural annotation of trajectories based on estimated local measures of velocity and turning angle, eventually with solar position covariate as a daytime indicator, ("Expectation-Maximization Binary Clustering for Behavioural Annotation").
Maintained by Joan Garriga. Last updated 1 years ago.
3.63 score 43 scriptsbioc
PANR:Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.
Maintained by Xin Wang. Last updated 5 months ago.
immunooncologynetworkinferencevisualizationgraphandnetworkclusteringcellbasedassays
3.30 score 2 scripts
astrezhnev
cjoint:AMCE Estimator for Conjoint Experiments
An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) <DOI:10.1093/pan/mpt024> Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
Maintained by Anton Strezhnev. Last updated 8 days ago.
3.29 score 29 scripts
cthombor
SafeVote:Election Vote Counting with Safety Features
Fork of 'vote_2.3-2', Raftery et al. (2021) <DOI:10.32614/RJ-2021-086>, with additional support for stochastic experimentation.
Maintained by Clark Thomborson. Last updated 6 months ago.
2.70 score 5 scripts
cran
Rlab:Functions and Datasets Required for ST370 Class
Provides functions and datasets required for the ST 370 course at North Carolina State University.
Maintained by Dennis Boos. Last updated 3 years ago.
2.42 score 8 dependentscran
falcon:Finding Allele-Specific Copy Number in Next-Generation Sequencing Data
This is a method for Allele-specific DNA Copy Number Profiling using Next-Generation Sequencing. Given the allele-specific coverage at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number. It requires, as input, the read counts for each variant allele in a pair of case and control samples. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.
Maintained by Hao Chen. Last updated 9 years ago.
1.78 score