Packages — R (Page 4 of 58)

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r-bionetstat 1.14.0

This package provides a package to perform differential network analysis, differential node analysis (differential coexpression analysis), network and metabolic pathways view. …

r-bioqc 1.22.0

BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that…

r-bios2cor 2.2

This package provides utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a…

r-biosigner 1.22.0

Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a method to…

r-biostrings 2.62.0

This package provides memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. …

r-biotip 1.8.0

This package adopts tipping-point theory to transcriptome profiles to help unravel disease regulatory trajectory. …

r-biotmle 1.18.0

This package provides tools for differential expression biomarker discovery based on microarray and next-generation sequencing data that leverage efficient semiparametric estimators of the average treatment effect for variable importance analysis. Estimation and…

r-biovizbase 1.42.0

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization.…

r-birewire 3.26.5

This package provides functions for bipartite network rewiring through N consecutive switching steps and for the computation of the minimal number of switching steps to be performed in order to maximise the…

r-birta 1.31.0

Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. "birta" (Bayesian Inference of Regulation of Transcriptional Activity) uses the…

r-biscuiteer 1.8.0

This package provides a test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age…

r-biscuiteerdata 1.6.0

This package contains default datasets used by the Bioconductor package biscuiteer. …

r-bisquerna 1.0.5

This package provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate…

r-bit 4.0.4

This package provides bitmapped vectors of booleans (no `NA's), coercion from and to logicals, integers and integer subscripts, fast boolean operators and fast summary statistics. With `bit' class vectors of true…

r-bit64 4.0.5

The bit64 package provides serializable S3 atomic 64 bit (signed) integers that can be used in vectors, matrices, arrays and `data.frames'. Methods are available for coercion from and to logicals, integers,…

r-bitops 1.0-7

This package provides functions for bitwise operations on integer vectors. …

r-blme 1.0-5

This package provides tools for maximum a posteriori estimation for linear and generalized linear mixed-effects models in a Bayesian setting. It extends the lme4 package. …

r-blob 1.2.3

Raw vectors in R are useful for storing a single binary object. What if you want to put a vector of them in a data frame? The blob package provides…

r-blockfest 2.0

This package provides an R implementation of an extension of the BayeScan software for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this…

r-blockmodeling 1.0.5

This package is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be…

r-bluster 1.4.0

This package wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering…

r-bmp 0.3

This package provides pure R tools to read BMP format images. It is currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images. …

r-boa 1.1.8-2

This package provides a menu-driven program and library of functions for carrying out convergence diagnostics and statistical and graphical analysis of "Markov chain Monte Carlo" (MCMC) sampling output. …

r-bookdown 0.25

This package provides output formats and utilities for authoring books and technical documents with R Markdown. …

r-boot 1.3-28

This package provides functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A.C. Davison and D.V. Hinkley (1997, CUP), originally written by Angelo Canty for…

r-bootstrap 2019.6

This package provides software and data for the book "An Introduction to the Bootstrap" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. This package is primarily provided…

r-boruta 7.0.0

This package provides an all relevant feature selection wrapper algorithm. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows). …

r-bqtl 1.0-33

This is a QTL mapping toolkit for inbred crosses and recombinant inbred lines. It includes maximum likelihood and Bayesian tools. …

r-brew 1.0-7

The brew package implements a templating framework for mixing text and R code for report generation. The template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's…

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 1.1.3

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 2.16.3

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 1.2-7

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 0.7.12

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 1.62.0

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-drerio-ucsc-danrer11 1.4.2

This package provides full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer11, May 2017) 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 0.3.1

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 1.30.0

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 1.36.0

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

r-bwstest 0.2.2

This package performs the Baumgartner-Weiss-Schindler two-sample test of equal probability distributions (doi:10.2307/2533862). It also performs similar rank-based tests for equal probability distributions due to Neuhauser (doi:10.1080/10485250108832874) and Murakami (doi:10.1080/00949655.2010.551516). …

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 1.5-15

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 0.3.3

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 3.0-12

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

r-cardata 3.0-5

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

r-caret 6.0-91

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

r-carrier 0.1.0

Sending functions to remote processes can be wasteful of resources because they carry their environments with them. With this package, it is easy to create functions that are isolated from their…

r-catalyst 1.18.1

This package is "Cytometry dATa anALYSis Tools" (CATALYST). Mass cytometry like "Cytometry by time of flight" (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby…

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 2.60.0

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-cccd 1.6

This package provides tools to create Class Cover Catch Digraphs, neighborhood graphs, and relatives. …

r-cdm 7.6-11

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-celldex 1.4.0

This package provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq. …

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 1.54.0

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

r-cghcall 2.56.0

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 3.46.0

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 1.22.0

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

r-chipcomp 1.24.0

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 1.18.0

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 3.28.1

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 1.30.3

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 1.44.0

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

r-chk 0.8.0

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-chorddiag 0.1.3

This package provides tools to create interactive chords diagrams via the D3 Javascript library. Chord diagrams show directed relationships among a group of entities. This package is based on `http://bl.ocks.org/mbostock/4062006'…

r-chromstar 1.20.2

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 1.16.0

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-chromvarmotifs 0.2.0-1.38bed55

This package stores motif collections as lists of "position frequency matrix" (PWMatrixList) objects provided by the `TFBSTools' package for use in R with packages like `motifmatchr' or `chromVAR'. …

r-chron 2.3-56

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

r-cicero 1.12.0

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

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