Packages — R (Page 4 of 51)

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r-brglm 0.7.2

Fit generalized linear models with binomial responses using either an adjusted-score approach to bias reduction or maximum penalized likelihood where penalization is by Jeffreys invariant prior. These procedures return estimates with improved…

r-bridgesampling 1.1-2

This package provides functions for estimating marginal likelihoods, Bayes factors, posterior model probabilities, and normalizing constants in general, via different versions of bridge sampling. …

r-brio 1.1.2

This package provides functions to handle basic input output. These functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings. …

r-brms 2.16.1

Fit Bayesian generalized (non-)linear multivariate multilevel models using 'Stan' for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others --…

r-brobdingnag 1.2-6

This package handles very large numbers in R. Real numbers are held using their natural logarithms, plus a logical flag indicating sign. The package includes a vignette that gives a…

r-broom 0.7.9

This package provides tools to convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like `dplyr', `tidyr'…

r-bseqsc 1.0-1.fef3f3e

BSeq-sc is a bioinformatics analysis pipeline that leverages single-cell sequencing data to estimate cell type proportion and cell type-specific gene expression differences from RNA-seq data from bulk tissue samples. This is…

r-bsgenome 1.60.0

This package provides infrastructure shared by all Biostrings-based genome data packages and support for efficient SNP representation. …

r-bsgenome-btaurus-ucsc-bostau8 1.4.2

This package provides the full genome sequences for Bos taurus (UCSC version bosTau8). …

r-bsgenome-celegans-ucsc-ce10 1.4.0

This package provides full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings objects. …

r-bsgenome-celegans-ucsc-ce6 1.4.0

This package provides full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects. …

r-bsgenome-dmelanogaster-ucsc-dm3 1.4.0

This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects. …

r-bsgenome-dmelanogaster-ucsc-dm3-masked 1.3.99

This package provides full masked genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm3, except…

r-bsgenome-dmelanogaster-ucsc-dm6 1.4.1

This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings objects. …

r-bsgenome-hsapiens-1000genomes-hs37d5 0.99.1

This package provides full genome sequences for Homo sapiens from 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37. …

r-bsgenome-hsapiens-ncbi-grch38 1.3.1000

This package provides full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects. …

r-bsgenome-hsapiens-ucsc-hg19 1.4.0

This package provides full genome sequences for Homo sapiens as provided by UCSC (hg19, February 2009) and stored in Biostrings objects. …

r-bsgenome-hsapiens-ucsc-hg19-masked 1.3.99

This package provides full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg19,…

r-bsgenome-hsapiens-ucsc-hg38 1.4.1

This package provides full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects. …

r-bsgenome-mmusculus-ucsc-mm10 1.4.0

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects. …

r-bsgenome-mmusculus-ucsc-mm9 1.4.0

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, July 2007) and stored in Biostrings objects. …

r-bsgenome-mmusculus-ucsc-mm9-masked 1.3.99

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9,…

r-bslib 0.3.0

This package simplifies custom CSS styling of both shiny and rmarkdown via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their various Bootswatch themes. An interactive…

r-bsseq 1.28.0

This package provides a collection of tools for analyzing and visualizing bisulfite sequencing data. …

r-btm 0.3.6

Biterm Topic Models find topics in collections of short texts. It is a word co-occurrence based topic model that learns topics by modeling word-word co-occurrences patterns which are called biterms. …

r-bumphunter 1.34.0

This package provides tools for finding bumps in genomic data in order to identify differentially methylated regions in epigenetic epidemiology studies. …

r-cachem 1.0.6

This package provides key-value stores with automatic pruning. Caches can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints. …

r-cairo 1.5-12.2

This package provides a Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). …

r-calculus 0.3.1

Efficient C++ optimized functions for numerical and symbolic calculus. It includes basic symbolic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion,…

r-calibrate 1.7.7

This is a package for drawing calibrated scales with tick marks on (non-orthogonal) variable vectors in scatterplots and biplots. …

r-callr 3.7.0

It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This package does exactly that. …

r-capushe 1.1.1

This package provides tools for the calibration of penalized criteria for model selection. The calibration methods available are based on the slope heuristics. …

r-car 3.0-11

This package provides functions and datasets from book Companion to Applied regression, Second Edition, Sage, 2011. …

r-cardata 3.0-4

This package provides datasets to accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage. …

r-caret 6.0-88

This package provides miscellaneous functions for training and plotting classification and regression models. …

r-catalyst 1.16.2

This package is Cytometry dATa anALYSis Tools (CATALYST). Mass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for…

r-catch 1.0-1.196ddd5

This package allows building the hierarchy of domains starting from Hi-C data. Each hierarchical level is identified by a minimum value of physical insulation between neighboring domains. …

r-catdap 1.3.5

This package provides functions for analyzing multivariate data. Dependencies of the distribution of the specified variable (response variable) to other variables (explanatory variables) are derived and evaluated by the "Akaike Information Criterion"…

r-category 2.58.0

This package provides a collection of tools for performing category analysis. …

r-catools 1.18.2

This package contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum,…

r-catterplots 0-3.ae17cd5

Did you ever wish you could make scatter plots with cat shaped points? Now you can! …

r-cdm 7.5-15

This package provides functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous item responses. It enables the estimation of the DINA and DINO model, the multiple group…

r-cellchat 1.0.0-1.21edd22

This package infers, visualizes and analyzes the cell-cell communication networks from scRNA-seq data. …

r-cellranger 1.1.0

This package provides helper functions to work with spreadsheets and the `A1:D10' style of cell range specification. …

r-centipede 1.2

CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions of the genome that are bound by particular transcription factors. It starts by identifying a set of candidate binding sites, and…

r-cgdsr 1.3.0

This package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC). …

r-cghbase 1.52.0

This package contains functions and classes that are needed by the `arrayCGH' packages. …

r-cghcall 2.54.0

This package contains functions and classes that are needed by `arrayCGH' packages. …

r-checkmate 2.0.0

This package provides tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead. …

r-chemminer 3.44.0

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. It contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and…

r-chemometricswithr 0.1.13

This package provides functions and scripts used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011). …

r-chicago 1.20.0

This package provides a pipeline for analysing Capture Hi-C data. …

r-chipcomp 1.22.0

ChIPComp implements a statistical method for quantitative comparison of multiple ChIP-seq datasets. It detects differentially bound sharp binding sites across multiple conditions considering matching control in ChIP-seq datasets. …

r-chipexoqual 1.16.0

This package provides a quality control pipeline for ChIP-exo/nexus sequencing data. …

r-chipkernels 1.1-1.c9cfcac

ChIPKernels is an R package for building different string kernels used for DNA Sequence analysis. A dictionary of the desired kernel must be built and this dictionary can be used for…

r-chippeakanno 3.26.4

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and…

r-chipseeker 1.28.3

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and…

r-chipseq 1.42.0

This package provides tools for processing short read data from ChIPseq experiments. …

r-chk 0.7.0

This is a package for developers to check user-supplied function arguments. It is designed to be simple, fast and customizable. Error messages follow the tidyverse style guide. …

r-chromstar 1.18.0

This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses. …

r-chromstardata 1.16.0

This package provides ChIP-seq data for demonstration purposes in the chromstaR package. …

r-chromvar 1.14.0

This package `r-chromvar' determines variation in chromatin accessibility across sets of annotations or peaks. `r-chromvar' is designed primarily for single-cell or sparse chromatin accessibility data like single cell assay for transposase-accessible chromatin…

r-chron 2.3-56

This package provides chronological R objects which can handle dates and times. …

r-cicero 1.10.1

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data. …

r-cicero-monocle3 1.3.2-1.fa2fb65

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data. …

r-circlize 0.4.13

Circular layout is an efficient way to visualise huge amounts of information. This package provides an implementation of circular layout generation in R as well as an enhancement of available software. …

r-circrnaprofiler 1.6.0

`r-circrnaprofiler' is a computational framework for a comprehensive in silico analysis of "circular RNA" (circRNAs). This computational framework allows combining and analyzing circRNAs previously detected by multiple publicly available annotation-based circRNA detection…

r-circular 0.4-93

This package provides tools for circular statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific. …

r-circus 0.1.5

Circus is an R package for annotation, analysis and visualization of circRNA data. Users can annotate their circRNA candidates with host genes, gene featrues they are spliced from, and discriminate between…

r-cistopic 2.1.0

The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as "Latent Dirichlet Allocation" (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single…

r-cistopic-next 0.3.0-1.04cecbb

The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as "Latent Dirichlet Allocation" (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single…

r-citr 0.3.2

This package provides functions and an RStudio add-in that search a BibTeX or BibLaTeX file to create and insert formatted Markdown citations into the current document. …

r-class 7.3-19

This package provides various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps. …

r-classint 0.4-3

This package provides selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes. …

r-cli 3.0.1

This package provides a suite of tools designed to build attractive command line interfaces (CLIs). It includes tools for drawing rules, boxes, trees, and Unicode symbols with ASCII alternatives. …

r-clipr 0.7.1

This package provides simple utility functions to read from and write to the system clipboards. …

r-clisymbols 1.2.0

This package provides a small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode. …

r-clubsandwich 0.5.3

Provides several cluster-robust variance estimators (i.e., sandwich estimators) for ordinary and weighted least squares linear regression models, including the bias-reduced linearization estimator introduced by Bell and McCaffrey (2002) `http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf' and developed further by Pustejovsky…

r-clue 0.3-59

Cluster ensembles are collections of individual solutions to a given clustering problem which are useful or necessary to consider in a wide range of applications. This R package provides an extensible…

r-cluster 2.1.2

This package provides methods for cluster analysis. It is a much extended version of the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding…

r-clusterexperiment 2.12.0

This package provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA expression data sets. …

r-clusterprofiler 4.0.5

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters. …

r-clusterr 1.2.5

This package provides Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes…

r-clusteval 0.1

This R package provides a suite of tools to evaluate clustering algorithms, clusterings, and individual clusters. …

r-clustree 0.4.3

Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number…

r-cmdfun 1.0.2

Writing interfaces to command line software is cumbersome. The cmdfun package provides a framework for building function calls to seamlessly interface with shell commands by allowing lazy evaluation of command line…

r-cmplot 3.6.2

Circle Manhattan Plot is an R package that can lay out genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's…

r-cmprsk 2.2-10

This package provides tool for estimation, testing and regression modeling of subdistribution functions in competing risks, as described in Gray (1988), A class of K-sample tests for comparing the cumulative incidence of…

r-cner 1.28.0

This package provides tools for large-scale identification and advanced visualization of sets of conserved noncoding elements. …

r-cobs 1.3-4

This package provides qualitatively constrained (regression) smoothing splines via linear programming and sparse matrices. …

r-coda 0.19-4

This package provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain. …

r-codedepends 0.6.5

This package provides tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of…

r-codetools 0.2-18

This package provides code analysis tools for R to check R code for possible problems. …

r-coin 1.4-1

This package provides conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems. …

r-collapsibletree 0.1.7

This is a package for interactive Reingold-Tilford tree diagrams created using D3.js, where every node can be expanded and collapsed by clicking on it. Tooltips and color gradients can be mapped to…

r-colorout 1.2-2

`colorout' is an R package that colorizes R output when running in terminal emulator. R STDOUT is parsed and numbers, negative numbers, dates in the standard format, strings, and R constants are identified…

r-colorramps 2.3

This package provides features to build gradient color maps. …

r-colorspace 2.0-2

This package carries out a mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL…

r-colourpicker 1.1.0

This package provides a color picker that can be used as an input in Shiny apps or Rmarkdown documents. The color picker supports alpha opacity, custom color palettes, and many more…

r-combinat 0.0-8

This package provides assorted routines for combinatorics. …

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