Packages — R (Page 7 of 11)

r-rtsne 0.15 — T-distributed stochastic neighbor embedding

This package provides an R wrapper around the fast T-distributed Stochastic Neighbor Embedding using a Barnes-Hut implementation.

r-runit 0.4.32 — R unit test framework

This package provides R functions implementing a standard unit testing framework, with additional code inspection and report generation tools.

r-ruvseq 1.16.0 — Remove unwanted variation from RNA-Seq data

This package implements methods to remove unwanted variation (RUV) of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

r-rversions 1.0.3 — Query R versions, including 'r-release' and 'r-oldrel'

This package provides functions to query the main R repository to find the versions that r-release and r-oldrel refer to, and also all previous R versions and their release dates.

r-rvest 0.3.2 — Simple web scraping for R

r-rvest helps you scrape information from web pages. It is designed to work with magrittr to make it easy to express common web scraping tasks, inspired by libraries like BeautifulSoup.

r-s4vectors 0.20.1 — S4 implementation of vectors and lists

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself.

r-sandwich 2.5-0 — Robust Covariance Matrix Estimators

This package provides model-robust standard error estimators for cross-sectional, time series, clustered, panel, and longitudinal data.

r-sapa 2.0-2 — Spectral analysis for physical applications

This package provides software for the book Spectral Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, Cambridge University Press, 1993.

r-savr 1.20.0 — Parse and analyze Illumina SAV files

This package provides tools to parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots.

r-scales 1.0.0 — Scale functions for visualization

This package provides graphical scales that map data to aesthetics, and provides methods for automatically determining breaks and labels for axes and legends.

r-scater 1.10.0 — Single-cell analysis toolkit for gene expression data in R

This package provides a collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.

r-scatterplot3d 0.3-41 — 3D scatter plot

This package provides an implementation of scatter plots for plotting. a three dimensional point cloud.

r-scran 1.10.1 — Methods for single-cell RNA-Seq data analysis

This package implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.

r-sdmtools 1.1-221 — Species distribution modelling tools

This packages provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time. It further includes methods for visualizing outcomes, selecting thresholds, calculating measures of accuracy and landscape fragmentation statistics, etc.

r-segmented 0.5-3.0 — Regression models with breakpoints estimation

Given a regression model, segmented updates the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.

r-selectr 0.4-1 — Translate CSS selectors to XPath expressions

r-selectr translates a CSS3 selector into an equivalent XPath expression. This allows you to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package cssselect.

r-sendmailr 1.2-1 — Send email using R

This package contains a simple SMTP client which provides a portable solution for sending email, including attachments, from within R.

r-seqgl 1.1.4 — Group lasso for Dnase/ChIP-seq data

SeqGL is a group lasso based algorithm to extract transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. This package presents a method which uses group lasso to discriminate between bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.

r-seqinr 3.4-5 — Biological sequences retrieval and analysis

This package provides tools for exploratory data analysis and data visualization of biological sequence (DNA and protein) data. It also includes utilities for sequence data management under the ACNUC system.

r-seqlogo 1.48.0 — Sequence logos for DNA sequence alignments

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

r-seqminer 6.1 — Read nucleotide sequence data (VCF, BCF, and METAL formats)

This package provides tools to integrate nucleotide sequencing data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.

r-seqpattern 1.14.0 — Visualising oligonucleotide patterns and motif occurrences

This package provides tools to visualize oligonucleotide patterns and sequence motif occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.

r-seriation 1.2-3 — Infrastructure for ordering objects using seriation

This package provides infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. It also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).

r-servr 0.11 — Simple HTTP server to serve static files or dynamic documents

Servr provides an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.

r-sessioninfo 1.1.1 — R session information

This package provides tools to query and print information about the current R session. It is similar to utils::sessionInfo(), but includes more information about packages, and where they were installed from.

r-seurat 2.3.4 — Seurat is an R toolkit for single cell genomics

This package is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.

r-sfsmisc 1.1-2 — Utilities from "Seminar fuer Statistik" ETH Zurich

This package provides useful utilities from Seminar fuer Statistik ETH Zurich, including many that are related to graphics.

r-shape 1.4.4 — Functions for plotting graphical shapes

This package provides functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...

r-shiny 1.1.0 — Easy interactive web applications with R

Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.

r-shinyace 0.3.2 — Ace editor bindings for Shiny

This package provides Ace editor bindings to enable a rich text editing environment within Shiny.

r-shinydashboard 0.7.1 — Create dashboards with shiny

This package provides an extension to the Shiny web application framework for R, making it easy to create attractive dashboards.

r-shinyfiles 0.7.2 — Server-side file system viewer for Shiny

This package provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to "download" files to a temporary location. Both file and folder selection as well as file saving is available.

r-shortread 1.40.0 — FASTQ input and manipulation tools

This package implements sampling, iteration, and input of FASTQ files. It 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.

r-signal 0.7-6 — Signal processing

This package provides a set of signal processing functions originally written for Matlab and GNU Octave. It includes filter generation utilities, filtering functions, resampling routines, and visualization of filter models. It also includes interpolation functions.

r-singlecellexperiment 1.4.0 — S4 classes for single cell data

This package defines an S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.

r-sjlabelled 1.0.14 — Labelled data utility functions

This package provides a collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.

r-sjmisc 2.7.6 — Data and variable transformation functions

This package is a collection of miscellaneous utility functions, supporting data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. The data transformation functions also support labelled data, and all integrate seamlessly into a tidyverse workflow.

r-sjplot 2.6.1 — Data visualization for statistics in social science

This package represents a collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.

r-sjstats 0.17.2 — Functions for common statistical computations

This package provides a collection of convenient functions for common statistical computations, which are not directly provided by R's base or stats packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort. Second, these shortcut functions are generic, and can be applied not only to vectors, but also to other objects as well. The focus of most functions lies on summary statistics or fit measures for regression models, including generalized linear models, mixed effects models and Bayesian models.

r-slam 0.1-43 — Sparse lightweight arrays and matrices

This package contains data structures and algorithms for sparse arrays and matrices, based on index arrays and simple triplet representations, respectively.

r-sm 2.2-5.6 — Smoothing methods for nonparametric regression and density estimation

This is software accompanying the book 'Applied Smoothing Techniques for Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford University Press. It provides smoothing methods for nonparametric regression and density estimation

r-smoother 1.1 — Functions relating to the smoothing of numerical data

This package provides a collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.

r-sn 1.5-3 — The skew-normal and skew-t distributions

This packages provides functionalities to build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provides related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.

r-sna 2.4 — Tools for social network analysis

This package provides a range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.

r-snakecase 0.9.2 — Convert strings into any case

This package provides a consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others.

r-snow 0.4-3 — Support for simple parallel computing in R

The snow package provides support for simple parallel computing on a network of workstations using R. A master R process calls makeCluster to start a cluster of worker processes; the master process then uses functions such as clusterCall and clusterApply to execute R code on the worker processes and collect and return the results on the master.

r-snowfall 1.84-6.1 — Easier cluster computing

This package is a usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. The package is also designed as connector to the cluster management tool sfCluster, but can also used without it.

r-snpstats 1.32.0 — Methods for SNP association studies

This package provides classes and statistical methods for large single-nucleotide polymorphism (SNP) association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

r-sourcetools 0.1.7 — Tools for reading, tokenizing and parsing R code

The sourcetools package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.

r-sp 1.3-1 — Classes and methods for spatial data

This package provides classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.

r-spams 2.6-2017-03-22 — Toolbox for solving sparse estimation problems

SPAMS (SPArse Modeling Software) is an optimization toolbox for solving various sparse estimation problems. It includes tools for the following problems:

  1. Dictionary learning and matrix factorization (NMF, sparse principle component analysis (PCA), ...)

  2. Solving sparse decomposition problems with LARS, coordinate descent, OMP, SOMP, proximal methods

  3. Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse group lasso, tree-structured regularization, structured sparsity with overlapping groups,...).

r-sparql 1.16 — SPARQL client for R

This package provides an interface to use SPARQL to pose SELECT or UPDATE queries to an end-point.

r-sparsem 1.77 — Sparse linear algebra

This package provides some basic linear algebra functionality for sparse matrices. It includes Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.

r-spatial 7.3-11 — Functions for kriging and point pattern analysis

This package provides functions for kriging and point pattern analysis.

r-splus2r 1.2-2 — Supplemental S-PLUS functionality in R

Currently there are many functions in S-PLUS that are missing in R. To facilitate the conversion of S-PLUS packages to R packages, this package provides some missing S-PLUS functionality in R.

r-sqldf 0.4-11 — Manipulate R data frames using SQL

The sqldf function is typically passed a single argument which is an SQL select statement where the table names are ordinary R data frame names. sqldf transparently sets up a database, imports the data frames into that database, performs the SQL statement and returns the result using a heuristic to determine which class to assign to each column of the returned data frame. The sqldf or read.csv.sql functions can also be used to read filtered files into R even if the original files are larger than R itself can handle.

r-squarem 2017.10-1 — Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms

This package provides algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette.

r-statmod 1.4.30 — Statistical modeling

This package provides a collection of algorithms and functions to aid statistical modeling. It includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. It also includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.

r-statnet-common 4.1.4 — R scripts and utilities used by the Statnet software

This package provides non-statistical utilities used by the software developed by the Statnet Project.

r-stringdist — Approximate string matching and string distance functions

This package implements an approximate string matching version of R's native match function. It can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.

r-stringi 1.2.4 — Character string processing facilities

This package allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g. via regular expressions), random string generation, string collation, transliteration, concatenation, date-time formatting and parsing, etc.

r-stringr 1.3.1 — Simple, consistent wrappers for common string operations

Stringr is a consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.

r-subplex 1.5-4 — Unconstrained optimization using the subplex algorithm

This package implements the Subplex optimization algorithm. It solves unconstrained optimization problems using a simplex method on subspaces. The method is well suited for optimizing objective functions that are noisy or are discontinuous at the solution.

r-summarizedexperiment 1.12.0 — Container for representing genomic ranges by sample

The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

r-summarytools 0.8.8 — Tools to quickly and neatly summarize data

This package provides tools for data frame summaries, cross-tabulations, weight-enabled frequency tables and common 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.

r-suppdists 1.1-9.4 — Supplementary distributions

This package provides ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions. In addition two random number generators of George Marsaglia are included.

r-survival 2.43-1 — Survival analysis

This package contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

r-sushi 1.20.0 — Tools for visualizing genomics data

This package provides flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures.

r-sva 3.30.0 — Surrogate variable analysis

This package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. It also contains functions for identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data like gene expression/RNA sequencing/methylation/brain imaging data that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise.

r-svdialogs 1.0.0 — Portable dialog boxes

This package helps to construct standard dialog boxes for your GUI, including message boxes, input boxes, list, file or directory selection, and others. In case R cannot display GUI dialog boxes, a simpler command line version of these interactive elements is also provided as a fallback solution.

r-svglite 1.2.1 — SVG graphics device

svglite is a graphics device that produces clean SVG (Scalable Vector Graphics) output, suitable for use on the web, or hand editing. Compared to the built-in svg(), svglite is considerably faster, produces smaller files, and leaves text as is.

r-svgui 1.0.0 — Functions for managing GUI clients in R

The SciViews svGUI package eases the management of Graphical User Interfaces (GUI) in R. It is independent from any particular GUI widgets. It centralizes info about GUI elements currently used, and it dispatches GUI calls to the particular toolkits in use in function of the context.

r-synchronicity 1.3.5 — Boost mutex functionality in R

This package provides support for synchronization via mutexes and may eventually support interprocess communication and message passing.

r-systempiper 1.16.0 — Next generation sequencing workflow and reporting environment

This R package provides tools for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure.

r-tclust 1.4-1 — Robust trimmed clustering

This package implements different robust clustering algorithms (tclust) based on trimming and including some graphical diagnostic tools (ctlcurves and DiscrFact).

r-testthat 2.0.1 — Unit testing for R

This package provides a unit testing system for R designed to be fun, flexible and easy to set up.

r-tgconfig — Infrastructure for managing package parameters

The goal of tgconfig is to provide infrastructure for managing package parameters.

r-tgstat 1.0.2-1.4f8e60c — Tanay's group statistical utilities

The goal of tgstat is to provide fast and efficient statistical tools.

r-th-data 1.0-9 — Shared data sets

This package contains supporting data sets that are used in other packages maintained by Torsten Hothorn.

r-tibble 1.4.2 — Simple data frames

This package provides a tbl_df class that offers better checking and printing capabilities than traditional data frames.

r-tidyr 0.8.2 — Tidy data with `spread()` and `gather()` functions

tidyr is a reframing of the reshape2 package designed to accompany the tidy data framework, and to work hand-in-hand with magrittr and dplyr to build a solid pipeline for data analysis. It is designed specifically for tidying data, not the general reshaping that reshape2 does, or the general aggregation that reshape did. In particular, built-in methods only work for data frames, and tidyr provides no margins or aggregation.

r-tidyselect 0.2.5 — Select from a set of strings

This package provides a backend for the selecting functions of the tidyverse. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other tidyverse interfaces for selection.

r-tidyverse 1.2.1 — Install and load packages from the "Tidyverse"

The tidyverse is a set of packages that work in harmony because they share common data representations and API design. This package is designed to make it easy to install and load multiple tidyverse packages in a single step.

r-timedate 3043.102 — Chronological and calendar objects

This package provides an environment for teaching "Financial Engineering and Computational Finance" and for managing chronological and calendar objects.

r-tinytex 0.9 — Helper functions for TeX Live and compiling LaTeX documents

This package provides helper functions to install and maintain the LaTeX distribution named TinyTeX, a lightweight, cross-platform, portable, and easy-to-maintain version of TeX Live. This package also contains helper functions to compile LaTeX documents, and install missing LaTeX packages automatically.

r-tmb 1.7.15 — Template model builder: a general random effect tool

With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines CppAD (C++ automatic differentiation), Eigen (templated matrix-vector library) and CHOLMOD (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through BLAS and parallel user templates.

r-topgo 2.34.0 — Enrichment analysis for gene ontology

The topGO package provides tools for testing gene ontology (GO) terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

r-trend 1.1.1 — Non-parametric trend tests and change-point detection

The analysis of environmental data often requires the detection of trends and change-points. This package includes tests for trend detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite) Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman correlation trend test), change-point detection (Lanzante's test procedures, Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two sample Robust Rank-Order Distributional Test.

r-trimcluster 0.1-2.1 — Cluster analysis with trimming

The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and Matran (1997). This optimizes the k-means criterion under trimming a portion of the points.

r-truncnorm 1.0-8 — Truncated normal distribution

This package provides functions for the truncated normal distribution with mean equal to mean and standard deviation equal to sd. It includes density, distribution, quantile, and expected value functions, as well as a random generation function.

r-tsa 1.2 — Time series analysis

This package contains R functions and datasets detailed in the book "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan.

r-tseries 0.10-45 — Time series analysis and computational finance

This package provides functions relating to time series analysis and computational finance.

r-tsne 0.1-3 — t-Distributed Stochastic Neighbor Embedding for R

This package provides a pure R implementation of the t-SNE algorithm.

r-tsp 1.1-6 — Traveling salesperson problem (TSP)

This package provides basic infrastructure and some algorithms for the traveling salesperson problem(TSP) (also known as the traveling salesman problem).

r-ttr 0.23-4 — Technical trading rules

This package provides functions and data to construct technical trading rules with R.

r-tweedie 2.3.2 — Evaluation of Tweedie exponential family models

Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), and related methods.

r-txdb-hsapiens-ucsc-hg19-knowngene 3.2.2 — Annotation package for human genome in TxDb format

This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg19 genome and based on the "knownGene" track. The database is exposed as a TxDb object.

r-txdb-mmusculus-ucsc-mm10-knowngene 3.4.4 — Annotation package for TxDb knownGene object(s) for Mouse

This package loads a TxDb object, which is an R interface to prefabricated databases contained in this package. This package provides the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) based on the knownGene track.

r-tximport 1.10.0 — Import and summarize transcript-level estimates for gene-level analysis

This package provides tools to import transcript-level abundance, estimated counts and transcript lengths, and to summarize them into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.

r-txtplot 1.0-3 — Text-based plotting

This package provides functions to produce rudimentary ASCII graphics directly in the terminal window. This package provides a basic plotting function (and equivalents of curve, density, acf and barplot) as well as a boxplot function.