R-universe search: needs:curl

r-lib

httr:Tools for Working with URLs and HTTP

Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).

Maintained by Hadley Wickham. Last updated 1 years ago.

api curl http

989 stars 20.56 score 29k scripts 4.3k dependents

tidyverse

tidyverse:Easily Install and Load 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. Learn more about the 'tidyverse' at <https://www.tidyverse.org>.

Maintained by Hadley Wickham. Last updated 5 months ago.

data-science tidyverse

1.7k stars 20.23 score 664k scripts 125 dependents

r-lib

devtools:Tools to Make Developing R Packages Easier

Collection of package development tools.

Maintained by Jennifer Bryan. Last updated 6 months ago.

package-creation

2.4k stars 19.55 score 51k scripts 150 dependents

plotly

plotly:Create Interactive Web Graphics via 'plotly.js'

Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.

Maintained by Carson Sievert. Last updated 4 months ago.

d3js data-visualization ggplot2 javascript plotly shiny webgl

2.6k stars 19.43 score 93k scripts 797 dependents

tidyverse

rvest:Easily Harvest (Scrape) Web Pages

Wrappers around the 'xml2' and 'httr' packages to make it easy to download, then manipulate, HTML and XML.

Maintained by Hadley Wickham. Last updated 5 months ago.

html web-scraping

1.5k stars 19.33 score 29k scripts 549 dependents

r-lib

pkgdown:Make Static HTML Documentation for a Package

Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.

Maintained by Hadley Wickham. Last updated 13 days ago.

documentation-tool

734 stars 18.46 score 588 scripts 162 dependents

rstudio

gt:Easily Create Presentation-Ready Display Tables

Build display tables from tabular data with an easy-to-use set of functions. With its progressive approach, we can construct display tables with a cohesive set of table parts. Table values can be formatted using any of the included formatting functions. Footnotes and cell styles can be precisely added through a location targeting system. The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.

Maintained by Richard Iannone. Last updated 26 days ago.

docx easy-to-use html latex rtf summary-tables

2.1k stars 18.36 score 20k scripts 112 dependents

bioc

Biostrings:Efficient manipulation of biological strings

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Maintained by Hervé Pagès. Last updated 1 months ago.

sequencematching alignment sequencing genetics dataimport datarepresentation infrastructure bioconductor-package core-package

62 stars 17.77 score 8.6k scripts 1.2k dependents

bioc

GenomicRanges:Representation and manipulation of genomic intervals

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.

Maintained by Hervé Pagès. Last updated 5 months ago.

genetics infrastructure datarepresentation sequencing annotation genomeannotation coverage bioconductor-package core-package

44 stars 17.68 score 13k scripts 1.3k dependents

r-lib

httr2:Perform HTTP Requests and Process the Responses

Tools for creating and modifying HTTP requests, then performing them and processing the results. 'httr2' is a modern re-imagining of 'httr' that uses a pipe-based interface and solves more of the problems that API wrapping packages face.

Maintained by Hadley Wickham. Last updated 4 days ago.

http

246 stars 17.64 score 1.9k scripts 1.1k dependents

r-lib

usethis:Automate Package and Project Setup

Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.

Maintained by Jennifer Bryan. Last updated 26 days ago.

github setup

869 stars 17.54 score 5.6k scripts 336 dependents

robjhyndman

forecast:Forecasting Functions for Time Series and Linear Models

Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.

Maintained by Rob Hyndman. Last updated 7 months ago.

forecast forecasting openblas cpp

1.1k stars 17.46 score 16k scripts 240 dependents

ropensci

magick:Advanced Graphics and Image-Processing in R

Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.

Maintained by Jeroen Ooms. Last updated 8 days ago.

image-manipulation image-processing imagemagick cpp

467 stars 17.38 score 9.0k scripts 258 dependents

gesistsa

rio:A Swiss-Army Knife for Data I/O

Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data format from the file extension, reasonable defaults are used for data import and export, web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly, and fast import packages are used where appropriate. An additional convenience function, 'convert()', provides a simple method for converting between file types.

Maintained by Chung-hong Chan. Last updated 3 months ago.

csv csvy data data-science excel io rio sas spss stata

610 stars 17.10 score 7.8k scripts 74 dependents

bioc

clusterProfiler:A universal enrichment tool for interpreting omics data

This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.

Maintained by Guangchuang Yu. Last updated 4 months ago.

annotation clustering genesetenrichment go kegg multiplecomparison pathways reactome visualization enrichment-analysis gsea

1.1k stars 17.03 score 11k scripts 48 dependents

ddsjoberg

gtsummary:Presentation-Ready Data Summary and Analytic Result Tables

Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers.

Maintained by Daniel D. Sjoberg. Last updated 6 days ago.

easy-to-use gt html5 regression-models reproducibility reproducible-research statistics summary-statistics summary-tables table1 tableone

1.1k stars 17.02 score 8.2k scripts 15 dependents

satijalab

Seurat:Tools for Single Cell Genomics

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Maintained by Paul Hoffman. Last updated 1 years ago.

human-cell-atlas single-cell-genomics single-cell-rna-seq cpp

2.4k stars 16.86 score 50k scripts 73 dependents

bioc

SummarizedExperiment:A container (S4 class) for matrix-like assays

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.

Maintained by Hervé Pagès. Last updated 5 months ago.

genetics infrastructure sequencing annotation coverage genomeannotation bioconductor-package core-package

34 stars 16.84 score 8.6k scripts 1.2k dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.

Maintained by Andri Signorell. Last updated 3 days ago.

fortran cpp

86 stars 16.73 score 7.7k scripts 101 dependents

bioc

GenomeInfoDb:Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

Maintained by Hervé Pagès. Last updated 2 months ago.

genetics datarepresentation annotation genomeannotation bioconductor-package core-package

32 stars 16.32 score 1.3k scripts 1.7k dependents

r-tmap

tmap:Thematic Maps

Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.

Maintained by Martijn Tennekes. Last updated 3 days ago.

choropleth-maps maps spatial thematic-maps visualisation

879 stars 16.25 score 13k scripts 24 dependents

joshuaulrich

quantmod:Quantitative Financial Modelling Framework

Specify, build, trade, and analyse quantitative financial trading strategies.

Maintained by Joshua M. Ulrich. Last updated 3 days ago.

algorithmic-trading charting data-import finance time-series

840 stars 16.18 score 8.1k scripts 343 dependents

bioc

DESeq2:Differential gene expression analysis based on the negative binomial distribution

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

Maintained by Michael Love. Last updated 26 days ago.

sequencing rnaseq chipseq geneexpression transcription normalization differentialexpression bayesian regression principalcomponent clustering immunooncology openblas cpp

375 stars 16.11 score 17k scripts 115 dependents

bioc

biomaRt:Interface to BioMart databases (i.e. Ensembl)

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<http://www.biomart.org>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.

Maintained by Mike Smith. Last updated 17 days ago.

annotation bioconductor biomart ensembl

38 stars 15.99 score 13k scripts 230 dependents

kassambara

survminer:Drawing Survival Curves using 'ggplot2'

Contains the function 'ggsurvplot()' for drawing easily beautiful and 'ready-to-publish' survival curves with the 'number at risk' table and 'censoring count plot'. Other functions are also available to plot adjusted curves for `Cox` model and to visually examine 'Cox' model assumptions.

Maintained by Alboukadel Kassambara. Last updated 5 months ago.

524 stars 15.87 score 7.0k scripts 55 dependents

jeroen

V8:Embedded JavaScript and WebAssembly Engine for R

An R interface to V8 <https://v8.dev>: Google's open source JavaScript and WebAssembly engine. This package can be compiled either with V8 version 6 and up or NodeJS when built as a shared library.

Maintained by Jeroen Ooms. Last updated 8 days ago.

javascript libv8 wasm nodejs cpp

201 stars 15.81 score 508 scripts 337 dependents

wilkelab

ggtext:Improved Text Rendering Support for 'ggplot2'

A 'ggplot2' extension that enables the rendering of complex formatted plot labels (titles, subtitles, facet labels, axis labels, etc.). Text boxes with automatic word wrap are also supported.

Maintained by Brenton M. Wiernik. Last updated 3 years ago.

657 stars 15.71 score 13k scripts 155 dependents

bioc

enrichplot:Visualization of Functional Enrichment Result

The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the 'clusterProfiler' package suite. All the visualization methods are developed based on 'ggplot2' graphics.

Maintained by Guangchuang Yu. Last updated 3 months ago.

annotation genesetenrichment go kegg pathways software visualization enrichment-analysis pathway-analysis

239 stars 15.71 score 3.1k scripts 58 dependents

r-lib

gh:'GitHub' 'API'

Minimal client to access the 'GitHub' 'API'.

Maintained by Gábor Csárdi. Last updated 2 months ago.

github github-api

224 stars 15.55 score 444 scripts 401 dependents

ropensci

rnaturalearth:World Map Data from Natural Earth

Facilitates mapping by making natural earth map data from <https://www.naturalearthdata.com/> more easily available to R users.

Maintained by Philippe Massicotte. Last updated 15 days ago.

peer-reviewed

234 stars 15.51 score 7.2k scripts 47 dependents

bioc

Rsamtools:Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.

dataimport sequencing coverage alignment qualitycontrol bioconductor-package core-package curl bzip2 xz-utils zlib cpp

28 stars 15.34 score 3.2k scripts 569 dependents

bioc

GenomicFeatures:Query the gene models of a given organism/assembly

Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.

Maintained by H. Pagès. Last updated 5 months ago.

genetics infrastructure annotation sequencing genomeannotation bioconductor-package core-package

26 stars 15.34 score 5.3k scripts 339 dependents

r-lib

covr:Test Coverage for Packages

Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' <https://about.codecov.io> or 'Coveralls' <https://coveralls.io>. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.

Maintained by Jim Hester. Last updated 2 months ago.

codecov coverage coverage-report travis-ci

337 stars 15.25 score 2.3k scripts 9 dependents

bioc

GenomicAlignments:Representation and manipulation of short genomic alignments

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Maintained by Hervé Pagès. Last updated 5 months ago.

infrastructure dataimport genetics sequencing rnaseq snp coverage alignment immunooncology bioconductor-package core-package

10 stars 15.21 score 3.1k scripts 528 dependents

sparklyr

sparklyr:R Interface to Apache Spark

R interface to Apache Spark, a fast and general engine for big data processing, see <https://spark.apache.org/>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.

Maintained by Edgar Ruiz. Last updated 14 days ago.

apache-spark distributed dplyr ide livy machine-learning remote-clusters spark sparklyr

959 stars 15.20 score 4.0k scripts 21 dependents

joshuaulrich

TTR:Technical Trading Rules

A collection of over 50 technical indicators for creating technical trading rules. The package also provides fast implementations of common rolling-window functions, and several volatility calculations.

Maintained by Joshua Ulrich. Last updated 1 years ago.

algorithmic-trading finance technical-analysis

338 stars 15.11 score 2.8k scripts 359 dependents

bioc

AnnotationDbi:Manipulation of SQLite-based annotations in Bioconductor

Implements a user-friendly interface for querying SQLite-based annotation data packages.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotation microarray sequencing genomeannotation bioconductor-package core-package

9 stars 15.05 score 3.6k scripts 769 dependents

bioc

DOSE:Disease Ontology Semantic and Enrichment analysis

This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.

Maintained by Guangchuang Yu. Last updated 5 months ago.

annotation visualization multiplecomparison genesetenrichment pathways software disease-ontology enrichment-analysis semantic-similarity

119 stars 14.97 score 2.0k scripts 61 dependents

tidyverse

googledrive:An Interface to Google Drive

Manage Google Drive files from R.

Maintained by Jennifer Bryan. Last updated 8 months ago.

google-drive

329 stars 14.97 score 2.1k scripts 164 dependents

bioc

MultiAssayExperiment:Software for the integration of multi-omics experiments in Bioconductor

Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.

Maintained by Marcel Ramos. Last updated 2 months ago.

infrastructure datarepresentation bioconductor bioconductor-package genomics nci-itcr tcga u24ca289073

71 stars 14.94 score 670 scripts 126 dependents

r-lib

gargle:Utilities for Working with Google APIs

Provides utilities for working with Google APIs <https://developers.google.com/apis-explorer>. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.

Maintained by Jennifer Bryan. Last updated 2 years ago.

authentication google

113 stars 14.90 score 266 scripts 192 dependents

rstudio

rsconnect:Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io', and 'RPubs'

Programmatic deployment interface for 'RPubs', 'shinyapps.io', and 'Posit Connect'. Supported content types include R Markdown documents, Shiny applications, Plumber APIs, plots, and static web content.

Maintained by Aron Atkins. Last updated 1 months ago.

141 stars 14.88 score 3.1k scripts 6 dependents

ropensci

gert:Simple Git Client for R

Simple git client for R based on 'libgit2' <https://libgit2.org> with support for SSH and HTTPS remotes. All functions in 'gert' use basic R data types (such as vectors and data-frames) for their arguments and return values. User credentials are shared with command line 'git' through the git-credential store and ssh keys stored on disk or ssh-agent.

Maintained by Jeroen Ooms. Last updated 7 days ago.

libgit2

154 stars 14.85 score 158 scripts 367 dependents

bioc

GSVA:Gene Set Variation Analysis for Microarray and RNA-Seq Data

Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.

Maintained by Robert Castelo. Last updated 11 days ago.

functionalgenomics microarray rnaseq pathways genesetenrichment gene-set-enrichment genomics pathway-enrichment-analysis

212 stars 14.74 score 1.6k scripts 19 dependents

florianhartig

DHARMa:Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models

The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Currently supported are linear and generalized linear (mixed) models from 'lme4' (classes 'lmerMod', 'glmerMod'), 'glmmTMB', 'GLMMadaptive', and 'spaMM'; phylogenetic linear models from 'phylolm' (classes 'phylolm' and 'phyloglm'); generalized additive models ('gam' from 'mgcv'); 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model classes. Moreover, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problems, such as over/underdispersion, zero-inflation, and residual spatial, phylogenetic and temporal autocorrelation.

Maintained by Florian Hartig. Last updated 28 days ago.

glmm regression regression-diagnostics residual

226 stars 14.74 score 2.8k scripts 10 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 6 days ago.

descriptive-statistics frequency-table html-report markdown pander pandoc pandoc-markdown rmarkdown rstudio

527 stars 14.62 score 2.9k scripts 6 dependents

tidyverse

googlesheets4:Access Google Sheets using the Sheets API V4

Interact with Google Sheets through the Sheets API v4 <https://developers.google.com/sheets/api>. "API" is an acronym for "application programming interface"; the Sheets API allows users to interact with Google Sheets programmatically, instead of via a web browser. The "v4" refers to the fact that the Sheets API is currently at version 4. This package can read and write both the metadata and the cell data in a Sheet.

Maintained by Jennifer Bryan. Last updated 8 months ago.

google-drive google-sheets spreadsheet

363 stars 14.55 score 7.0k scripts 142 dependents

ropensci

osmdata:Import 'OpenStreetMap' Data as Simple Features or Spatial Objects

Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server (<https://overpass-api.de/>) and processed with very fast 'C++' routines for return to 'R'.

Maintained by Mark Padgham. Last updated 2 months ago.

open0street0map openstreetmap overpass0api osm cpp osm-data overpass-api peer-reviewed cpp

322 stars 14.53 score 2.8k scripts 14 dependents

bioc

TCGAbiolinks:TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

Maintained by Tiago Chedraoui Silva. Last updated 1 months ago.

dnamethylation differentialmethylation generegulation geneexpression methylationarray differentialexpression pathways network sequencing survival software bioc bioconductor gdc integrative-analysis tcga tcga-data tcgabiolinks

310 stars 14.47 score 1.6k scripts 6 dependents

rstudio

plumber:An API Generator for R

Gives the ability to automatically generate and serve an HTTP API from R functions using the annotations in the R documentation around your functions.

Maintained by Barret Schloerke. Last updated 20 days ago.

api api-server plumber

1.4k stars 14.47 score 2.2k scripts 16 dependents

bioc

xcms:LC-MS and GC-MS Data Analysis

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

Maintained by Steffen Neumann. Last updated 18 days ago.

immunooncology massspectrometry metabolomics bioconductor feature-detection mass-spectrometry peak-detection cpp

196 stars 14.31 score 984 scripts 11 dependents

talgalili

heatmaply:Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2'

Create interactive cluster 'heatmaps' that can be saved as a stand- alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' to 'heatmap.2' with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'.

Maintained by Tal Galili. Last updated 9 months ago.

d3-heatmap dendextend dendrogram ggplot2 heatmap plotly

386 stars 14.21 score 2.0k scripts 45 dependents

business-science

timetk:A Tool Kit for Working with Time Series

Easy visualization, wrangling, and feature engineering of time series data for forecasting and machine learning prediction. Consolidates and extends time series functionality from packages including 'dplyr', 'stats', 'xts', 'forecast', 'slider', 'padr', 'recipes', and 'rsample'.

Maintained by Matt Dancho. Last updated 1 years ago.

coercion coercion-functions data-mining dplyr forecast forecasting forecasting-models machine-learning series-decomposition series-signature tibble tidy tidyquant tidyverse time time-series timeseries

626 stars 14.20 score 4.0k scripts 16 dependents

rstudio

pins:Pin, Discover, and Share Resources

Publish data sets, models, and other R objects, making it easy to share them across projects and with your colleagues. You can pin objects to a variety of "boards", including local folders (to share on a networked drive or with 'DropBox'), 'Posit Connect', 'AWS S3', and more.

Maintained by Julia Silge. Last updated 2 months ago.

azure gcloud rpins rsconnect s3 storage

321 stars 14.17 score 1.9k scripts 17 dependents

dkahle

ggmap:Spatial Visualization with ggplot2

A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.

Maintained by David Kahle. Last updated 1 years ago.

770 stars 14.17 score 12k scripts 31 dependents

doi-usgs

dataRetrieval:Retrieval Functions for USGS and EPA Hydrology and Water Quality Data

Collection of functions to help retrieve U.S. Geological Survey and U.S. Environmental Protection Agency water quality and hydrology data from web services. Data are discovered from National Water Information System <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>. Water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.

Maintained by Laura DeCicco. Last updated 5 days ago.

usgs

286 stars 14.16 score 1.7k scripts 15 dependents

bioc

GOSemSim:GO-terms Semantic Similarity Measures

The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.

Maintained by Guangchuang Yu. Last updated 5 months ago.

annotation go clustering pathways network software bioinformatics gene-ontology semantic-similarity cpp

63 stars 14.12 score 708 scripts 68 dependents

bioc

BSgenome:Software infrastructure for efficient representation of full genomes and their SNPs

Infrastructure shared by all the Biostrings-based genome data packages.

Maintained by Hervé Pagès. Last updated 2 months ago.

genetics infrastructure datarepresentation sequencematching annotation snp bioconductor-package core-package

9 stars 14.12 score 1.2k scripts 267 dependents

leifeld

texreg:Conversion of R Regression Output to LaTeX or HTML Tables

Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented. Details can be found in Leifeld (2013), JStatSoft <doi:10.18637/jss.v055.i08>.)

Maintained by Philip Leifeld. Last updated 3 months ago.

html-tables latex latex-tables regression reporting table texreg

113 stars 14.09 score 1.8k scripts 67 dependents

bioc

ensembldb:Utilities to create and use Ensembl-based annotation databases

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

Maintained by Johannes Rainer. Last updated 5 months ago.

genetics annotationdata sequencing coverage annotation bioconductor bioconductor-packages ensembl

35 stars 14.08 score 892 scripts 108 dependents

ropensci

crul:HTTP Client

A simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>). The package name is a play on curl, the widely used command line tool for HTTP, and this package is built on top of the R package 'curl', an interface to 'libcurl' (<https://curl.se/libcurl/>).

Maintained by Scott Chamberlain. Last updated 8 months ago.

http https api web-services curl download libcurl async mocking caching

107 stars 14.07 score 240 scripts 168 dependents

walkerke

tidycensus:Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames

An integrated R interface to several United States Census Bureau APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping and spatial analysis.

Maintained by Kyle Walker. Last updated 2 months ago.

648 stars 14.02 score 7.5k scripts 10 dependents

rstudio

chromote:Headless Chrome Web Browser Interface

An implementation of the 'Chrome DevTools Protocol', for controlling a headless Chrome web browser.

Maintained by Garrick Aden-Buie. Last updated 5 days ago.

164 stars 13.96 score 162 scripts 28 dependents

jbkunst

highcharter:A Wrapper for the 'Highcharts' Library

A wrapper for the 'Highcharts' library including shortcut functions to plot R objects. 'Highcharts' <https://www.highcharts.com/> is a charting library offering numerous chart types with a simple configuration syntax.

Maintained by Joshua Kunst. Last updated 1 years ago.

highcharts htmlwidgets shiny shiny-r visualization wrapper

725 stars 13.93 score 4.9k scripts 18 dependents

bioc

phyloseq:Handling and analysis of high-throughput microbiome census data

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

Maintained by Paul J. McMurdie. Last updated 5 months ago.

immunooncology sequencing microbiome metagenomics clustering classification multiplecomparison geneticvariability

600 stars 13.91 score 8.4k scripts 38 dependents

bioc

AnnotationHub:Client to access AnnotationHub resources

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

infrastructure dataimport gui thirdpartyclient core-package u24ca289073

17 stars 13.88 score 2.7k scripts 104 dependents

config-i1

smooth:Forecasting Using State Space Models

Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting. The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>), Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>), SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>), Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>), Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>) and several simulation functions. It also allows dealing with intermittent demand based on the iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).

Maintained by Ivan Svetunkov. Last updated 1 days ago.

arima arima-forecasting ces ets exponential-smoothing forecast state-space time-series openblas cpp

90 stars 13.83 score 412 scripts 25 dependents

bioc

BiocFileCache:Manage Files Across Sessions

This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

Maintained by Lori Shepherd. Last updated 2 months ago.

dataimport core-package u24ca289073

13 stars 13.76 score 486 scripts 436 dependents

ropensci

rentrez:'Entrez' in R

Provides an R interface to the NCBI's 'EUtils' API, allowing users to search databases like 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and 'PubMed' <https://pubmed.ncbi.nlm.nih.gov/>, process the results of those searches and pull data into their R sessions.

Maintained by David Winter. Last updated 4 years ago.

199 stars 13.72 score 784 scripts 98 dependents

ropensci

taxize:Taxonomic Information from Around the Web

Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.

Maintained by Zachary Foster. Last updated 27 days ago.

taxonomy biology nomenclature json api web api-client identifiers species names api-wrapper biodiversity darwincore data taxize

274 stars 13.63 score 1.6k scripts 23 dependents

bioc

SingleCellExperiment:S4 Classes for Single Cell Data

Defines a 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.

Maintained by Davide Risso. Last updated 24 days ago.

immunooncology datarepresentation dataimport infrastructure singlecell

13.53 score 15k scripts 285 dependents

bioc

KEGGREST:Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)

A package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Only for academic use by academic users belonging to academic institutions (see <https://www.kegg.jp/kegg/rest/>). Note that KEGGREST is based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotation pathways thirdpartyclient kegg bioconductor-package core-package

10 stars 13.50 score 688 scripts 771 dependents

bioc

GEOquery:Get data from NCBI Gene Expression Omnibus (GEO)

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

Maintained by Sean Davis. Last updated 5 months ago.

microarray dataimport onechannel twochannel sage bioconductor bioinformatics data-science genomics ncbi-geo

93 stars 13.48 score 4.1k scripts 45 dependents

bioc

RCy3:Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Maintained by Alex Pico. Last updated 5 days ago.

visualization graphandnetwork thirdpartyclient network

52 stars 13.47 score 628 scripts 17 dependents

ropensci

RSelenium:R Bindings for 'Selenium WebDriver'

Provides a set of R bindings for the 'Selenium 2.0 WebDriver' (see <https://www.selenium.dev/documentation/> for more information) using the 'JsonWireProtocol' (see <https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol> for more information). 'Selenium 2.0 WebDriver' allows driving a web browser natively as a user would either locally or on a remote machine using the Selenium server it marks a leap forward in terms of web browser automation. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.

Maintained by Jonathan Völkle. Last updated 2 years ago.

rselenium selenium webdriver

344 stars 13.38 score 1.9k scripts 12 dependents

business-science

tidyquant:Tidy Quantitative Financial Analysis

Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.

Maintained by Matt Dancho. Last updated 2 months ago.

dplyr financial-analysis financial-data financial-statements multiple-stocks performance-analysis performanceanalytics quantmod stock stock-exchanges stock-indexes stock-lists stock-performance stock-prices stock-symbol tidyverse time-series timeseries xts

872 stars 13.34 score 5.2k scripts

dreamrs

esquisse:Explore and Visualize Your Data Interactively

A 'shiny' gadget to create 'ggplot2' figures interactively with drag-and-drop to map your variables to different aesthetics. You can quickly visualize your data accordingly to their type, export in various formats, and retrieve the code to reproduce the plot.

Maintained by Victor Perrier. Last updated 1 months ago.

addin data-visualization ggplot2 rstudio-addin visualization

1.8k stars 13.31 score 1.1k scripts 1 dependents

ropensci

rgbif:Interface to the Global Biodiversity Information Facility API

A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/developer/summary>). GBIF is a database of species occurrence records from sources all over the globe. rgbif includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.

Maintained by John Waller. Last updated 18 days ago.

gbif specimens api web-services occurrences species taxonomy biodiversity data lifewatch oscibio spocc

161 stars 13.26 score 2.1k scripts 20 dependents

oscarkjell

text:Analyses of Text using Transformers Models from HuggingFace, Natural Language Processing and Machine Learning

Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.

Maintained by Oscar Kjell. Last updated 9 days ago.

deep-learning machine-learning nlp transformers openjdk

145 stars 13.21 score 436 scripts 1 dependents

bioc

dada2:Accurate, high-resolution sample inference from amplicon sequencing data

The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.

Maintained by Benjamin Callahan. Last updated 5 months ago.

immunooncology microbiome sequencing classification metagenomics amplicon bioconductor bioinformatics metabarcoding taxonomy cpp

487 stars 13.17 score 3.0k scripts 4 dependents

ropensci

pdftools:Text Extraction, Rendering and Converting of PDF Documents

Utilities based on 'libpoppler' <https://poppler.freedesktop.org> for extracting text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.

Maintained by Jeroen Ooms. Last updated 28 days ago.

pdf-files pdf-format pdftools poppler poppler-library text-extraction cpp

529 stars 13.10 score 3.3k scripts 47 dependents

bioc

scran:Methods for Single-Cell RNA-Seq Data Analysis

Implements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and other common tasks in routine single-cell analysis workflows.

Maintained by Aaron Lun. Last updated 5 months ago.

immunooncology normalization sequencing rnaseq software geneexpression transcriptomics singlecell clustering bioconductor-package human-cell-atlas single-cell-rna-seq openblas cpp

41 stars 13.05 score 7.6k scripts 37 dependents

keaven

gsDesign:Group Sequential Design

Derives group sequential clinical trial designs and describes their properties. Particular focus on time-to-event, binary, and continuous outcomes. Largely based on methods described in Jennison, Christopher and Turnbull, Bruce W., 2000, "Group Sequential Methods with Applications to Clinical Trials" ISBN: 0-8493-0316-8.

Maintained by Keaven Anderson. Last updated 27 days ago.

biostatistics boundaries clinical-trials design spending-functions

51 stars 13.05 score 338 scripts 5 dependents

bioc

Gviz:Plotting data and annotation information along genomic coordinates

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

Maintained by Robert Ivanek. Last updated 5 months ago.

visualization microarray sequencing

79 stars 13.05 score 1.4k scripts 46 dependents

bioc

ChIPseeker:ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

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 incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Maintained by Guangchuang Yu. Last updated 5 months ago.

annotation chipseq software visualization multiplecomparison atac-seq chip-seq comparison epigenetics epigenomics

233 stars 13.05 score 1.6k scripts 5 dependents

ropensci

piggyback:Managing Larger Data on a GitHub Repository

Helps store files as GitHub release assets, which is a convenient way for large/binary data files to piggyback onto public and private GitHub repositories. Includes functions for file downloads, uploads, and managing releases via the GitHub API.

Maintained by Carl Boettiger. Last updated 4 months ago.

data-store git-lfs peer-reviewed

187 stars 12.98 score 187 scripts 12 dependents

tidyverse

ellmer:Chat with Large Language Models

Chat with large language models from a range of providers including 'Claude' <https://claude.ai>, 'OpenAI' <https://chatgpt.com>, and more. Supports streaming, asynchronous calls, tool calling, and structured data extraction.

Maintained by Hadley Wickham. Last updated 3 days ago.

407 stars 12.94 score 98 scripts 8 dependents

michaelhallquist

MplusAutomation:An R Package for Facilitating Large-Scale Latent Variable Analyses in Mplus

Leverages the R language to automate latent variable model estimation and interpretation using 'Mplus', a powerful latent variable modeling program developed by Muthen and Muthen (<https://www.statmodel.com>). Specifically, this package provides routines for creating related groups of models, running batches of models, and extracting and tabulating model parameters and fit statistics.

Maintained by Michael Hallquist. Last updated 6 days ago.

86 stars 12.92 score 664 scripts 13 dependents

walkerke

tigris:Load Census TIGER/Line Shapefiles

Download TIGER/Line shapefiles from the United States Census Bureau (<https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>) and load into R as 'sf' objects.

Maintained by Kyle Walker. Last updated 5 months ago.

331 stars 12.87 score 5.3k scripts 16 dependents

rinterface

bs4Dash:A 'Bootstrap 4' Version of 'shinydashboard'

Make 'Bootstrap 4' Shiny dashboards. Use the full power of 'AdminLTE3', a dashboard template built on top of 'Bootstrap 4' <https://github.com/ColorlibHQ/AdminLTE>.

Maintained by David Granjon. Last updated 7 months ago.

bootstrap4 dashboard-templates hacktoberfest2022 shiny shiny-apps shinydashboard

442 stars 12.87 score 1.2k scripts 15 dependents

bioc

iSEE:Interactive SummarizedExperiment Explorer

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Maintained by Kevin Rue-Albrecht. Last updated 26 days ago.

cellbasedassays clustering dimensionreduction featureextraction geneexpression gui immunooncology shinyapps singlecell transcription transcriptomics visualization dimension-reduction feature-extraction gene-expression hacktoberfest human-cell-atlas shiny single-cell

225 stars 12.86 score 380 scripts 9 dependents

paleolimbot

ggspatial:Spatial Data Framework for ggplot2

Spatial data plus the power of the ggplot2 framework means easier mapping when input data are already in the form of spatial objects.

Maintained by Dewey Dunnington. Last updated 2 years ago.

379 stars 12.85 score 4.1k scripts 24 dependents

markedmondson1234

googleAuthR:Authenticate and Create Google APIs

Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility.

Maintained by Erik Grönroos. Last updated 10 months ago.

api authentication google googleauthr oauth2-flow shiny

178 stars 12.85 score 804 scripts 13 dependents

jtextor

dagitty:Graphical Analysis of Structural Causal Models

A port of the web-based software 'DAGitty', available at <https://dagitty.net>, for analyzing structural causal models (also known as directed acyclic graphs or DAGs). This package computes covariate adjustment sets for estimating causal effects, enumerates instrumental variables, derives testable implications (d-separation and vanishing tetrads), generates equivalent models, and includes a simple facility for data simulation.

Maintained by Johannes Textor. Last updated 4 months ago.

302 stars 12.83 score 1.7k scripts 11 dependents

bioc

SingleR:Reference-Based Single-Cell RNA-Seq Annotation

Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.

Maintained by Aaron Lun. Last updated 1 months ago.

software singlecell geneexpression transcriptomics classification clustering annotation bioconductor singler cpp

184 stars 12.83 score 2.1k scripts 2 dependents

bioc

minfi:Analyze Illumina Infinium DNA methylation arrays

Tools to analyze & visualize Illumina Infinium methylation arrays.

Maintained by Kasper Daniel Hansen. Last updated 4 months ago.

immunooncology dnamethylation differentialmethylation epigenetics microarray methylationarray multichannel twochannel dataimport normalization preprocessing qualitycontrol

60 stars 12.82 score 996 scripts 27 dependents

bioc

MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics

MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

Maintained by Laurent Gatto. Last updated 17 days ago.

immunooncology infrastructure proteomics massspectrometry qualitycontrol dataimport bioconductor bioinformatics mass-spectrometry proteomics-data visualisation cpp

131 stars 12.76 score 772 scripts 36 dependents

bioc

plyranges:A fluent interface for manipulating GenomicRanges

A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.

Maintained by Michael Love. Last updated 13 days ago.

infrastructure datarepresentation workflowstep coverage bioconductor data-analysis dplyr genomic-ranges genomics tidy-data

144 stars 12.66 score 1.9k scripts 20 dependents

bioc

rtracklayer:R interface to genome annotation files and the UCSC genome browser

Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

Maintained by Michael Lawrence. Last updated 6 days ago.

annotation visualization dataimport zlib openssl curl

12.66 score 6.7k scripts 480 dependents

insightsengineering

teal:Exploratory Web Apps for Analyzing Clinical Trials Data

A 'shiny' based interactive exploration framework for analyzing clinical trials data. 'teal' currently provides a dynamic filtering facility and different data viewers. 'teal' 'shiny' applications are built using standard 'shiny' modules.

Maintained by Dawid Kaledkowski. Last updated 1 months ago.

clinical-trials nest shiny webapp

206 stars 12.65 score 176 scripts 5 dependents

bioc

SpatialExperiment:S4 Class for Spatially Resolved -omics Data

Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.

Maintained by Dario Righelli. Last updated 5 months ago.

datarepresentation dataimport infrastructure immunooncology geneexpression transcriptomics singlecell spatial

59 stars 12.63 score 1.8k scripts 71 dependents

hrbrmstr

ggalt:Extra Coordinate Systems, 'Geoms', Statistical Transformations, Scales and Fonts for 'ggplot2'

A compendium of new geometries, coordinate systems, statistical transformations, scales and fonts for 'ggplot2', including splines, 1d and 2d densities, univariate average shifted histograms, a new map coordinate system based on the 'PROJ.4'-library along with geom_cartogram() that mimics the original functionality of geom_map(), formatters for "bytes", a stat_stepribbon() function, increased 'plotly' compatibility and the 'StateFace' open source font 'ProPublica'. Further new functionality includes lollipop charts, dumbbell charts, the ability to encircle points and coordinate-system-based text annotations.

Maintained by Bob Rudis. Last updated 2 years ago.

geom ggplot-extension ggplot2 ggplot2-geom ggplot2-scales

676 stars 12.60 score 2.3k scripts 7 dependents

wilkox

treemapify:Draw Treemaps in 'ggplot2'

Provides 'ggplot2' geoms for drawing treemaps.

Maintained by David Wilkins. Last updated 10 months ago.

data-visualisation ggplot2 treemap

215 stars 12.58 score 1.6k scripts 9 dependents

massimoaria

bibliometrix:Comprehensive Science Mapping Analysis

Tool for quantitative research in scientometrics and bibliometrics. It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>. 'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS', 'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions' (<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>), and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.

Maintained by Massimo Aria. Last updated 12 days ago.

bibliometric-analysis bibliometrics citation citation-network citations co-authors co-occurence co-word-analysis correspondence-analysis coupling isi-web journal manuscript quantitative-analysis scholars science science-mapping scientific scientometrics scopus

545 stars 12.54 score 518 scripts 2 dependents

bioc

microbiome:Microbiome Analytics

Utilities for microbiome analysis.

Maintained by Leo Lahti. Last updated 5 months ago.

metagenomics microbiome sequencing systemsbiology hitchip hitchip-atlas human-microbiome microbiology microbiome-analysis phyloseq population-study

293 stars 12.51 score 2.0k scripts 5 dependents

r-dbi

bigrquery:An Interface to Google's 'BigQuery' 'API'

Easily talk to Google's 'BigQuery' database from R.

Maintained by Hadley Wickham. Last updated 1 months ago.

bigquery database cpp

520 stars 12.47 score 1.8k scripts 4 dependents

cloudyr

aws.s3:'AWS S3' Client Package

A simple client package for the Amazon Web Services ('AWS') Simple Storage Service ('S3') 'REST' 'API' <https://aws.amazon.com/s3/>.

Maintained by Simon Urbanek. Last updated 5 years ago.

amazon aws aws-s3 cloudyr s3 s3-storage

383 stars 12.47 score 1.4k scripts 17 dependents

r-lib

credentials:Tools for Managing SSH and Git Credentials

Setup and retrieve HTTPS and SSH credentials for use with 'git' and other services. For HTTPS remotes the package interfaces the 'git-credential' utility which 'git' uses to store HTTP usernames and passwords. For SSH remotes we provide convenient functions to find or generate appropriate SSH keys. The package both helps the user to setup a local git installation, and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.

Maintained by Jeroen Ooms. Last updated 6 months ago.

git password ssh

72 stars 12.40 score 91 scripts 380 dependents

bioc

scDblFinder:scDblFinder

The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, the new fast and comprehensive scDblFinder method, and a reimplementation of the Amulet detection method for single-cell ATAC-seq.

Maintained by Pierre-Luc Germain. Last updated 12 days ago.

preprocessing singlecell rnaseq atacseq doublets single-cell

184 stars 12.38 score 888 scripts 1 dependents

bioc

TFBSTools:Software Package for Transcription Factor Binding Site (TFBS) Analysis

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

Maintained by Ge Tan. Last updated 19 days ago.

motifannotation generegulation motifdiscovery transcription alignment

28 stars 12.36 score 1.1k scripts 18 dependents

ouhscbbmc

REDCapR:Interaction Between R and REDCap

Encapsulates functions to streamline calls from R to the REDCap API. REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.

Maintained by Will Beasley. Last updated 3 months ago.

redcap redcap-api

118 stars 12.36 score 438 scripts 6 dependents

r-lib

rcmdcheck:Run 'R CMD check' from 'R' and Capture Results

Run 'R CMD check' from 'R' and capture the results of the individual checks. Supports running checks in the background, timeouts, pretty printing and comparing check results.

Maintained by Gábor Csárdi. Last updated 6 months ago.

116 stars 12.34 score 102 scripts 158 dependents

ropensci

stplanr:Sustainable Transport Planning

Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. The package was originally developed to support the 'Propensity to Cycle Tool', a publicly available strategic cycle network planning tool (Lovelace et al. 2017) <doi:10.5198/jtlu.2016.862>, but has since been extended to support public transport routing and accessibility analysis (Moreno-Monroy et al. 2017) <doi:10.1016/j.jtrangeo.2017.08.012> and routing with locally hosted routing engines such as 'OSRM' (Lowans et al. 2023) <doi:10.1016/j.enconman.2023.117337>. The main functions are for creating and manipulating geographic "desire lines" from origin-destination (OD) data (building on the 'od' package); calculating routes on the transport network locally and via interfaces to routing services such as <https://cyclestreets.net/> (Desjardins et al. 2021) <doi:10.1007/s11116-021-10197-1>; and calculating route segment attributes such as bearing. The package implements the 'travel flow aggregration' method described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779> and the 'OD jittering' method described in Lovelace et al. (2022) <doi:10.32866/001c.33873>. Further information on the package's aim and scope can be found in the vignettes and in a paper in the R Journal (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>, and in a paper outlining the landscape of open source software for geographic methods in transport planning (Lovelace, 2021) <doi:10.1007/s10109-020-00342-2>.

Maintained by Robin Lovelace. Last updated 7 months ago.

cycle cycling desire-lines origin-destination peer-reviewed pubic-transport route-network routes routing spatial transport transport-planning transportation walking

427 stars 12.31 score 684 scripts 3 dependents

nflverse

nflreadr:Download 'nflverse' Data

A minimal package for downloading data from 'GitHub' repositories of the 'nflverse' project.

Maintained by Tan Ho. Last updated 4 months ago.

nfl nflfastr nflverse sports-data

67 stars 12.29 score 476 scripts 10 dependents

bioc

bsseq:Analyze, manage and store whole-genome methylation data

A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.

Maintained by Kasper Daniel Hansen. Last updated 4 months ago.

dnamethylation cpp

37 stars 12.26 score 676 scripts 15 dependents

bioc

ReactomePA:Reactome Pathway Analysis

This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. This package is not affiliated with the Reactome team.

Maintained by Guangchuang Yu. Last updated 5 months ago.

pathways visualization annotation multiplecomparison genesetenrichment reactome enrichment-analysis reactome-pathway-analysis reactomepa

40 stars 12.25 score 1.5k scripts 7 dependents

bioc

ggbio:Visualization tools for genomic data

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

Maintained by Michael Lawrence. Last updated 5 months ago.

infrastructure visualization

111 stars 12.23 score 734 scripts 16 dependents

steffenmoritz

imputeTS:Time Series Missing Value Imputation

Imputation (replacement) of missing values in univariate time series. Offers several imputation functions and missing data plots. Available imputation algorithms include: 'Mean', 'LOCF', 'Interpolation', 'Moving Average', 'Seasonal Decomposition', 'Kalman Smoothing on Structural Time Series models', 'Kalman Smoothing on ARIMA models'. Published in Moritz and Bartz-Beielstein (2017) <doi:10.32614/RJ-2017-009>.

Maintained by Steffen Moritz. Last updated 3 years ago.

data-visualization imputation imputation-algorithm imputets missing-data time-series cpp

162 stars 12.18 score 1.9k scripts 27 dependents

stuart-lab

Signac:Analysis of Single-Cell Chromatin Data

A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.

Maintained by Tim Stuart. Last updated 7 months ago.

atac bioinformatics single-cell zlib cpp

355 stars 12.18 score 3.7k scripts 1 dependents

bioc

glmGamPoi:Fit a Gamma-Poisson Generalized Linear Model

Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.

Maintained by Constantin Ahlmann-Eltze. Last updated 15 days ago.

regression rnaseq software singlecell gamma-poisson glm negative-binomial-regression on-disk openblas cpp

111 stars 12.16 score 1.0k scripts 4 dependents

yihui

animation:A Gallery of Animations in Statistics and Utilities to Create Animations

Provides functions for animations in statistics, covering topics in probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions may be helpful in teaching statistics and data analysis. Also provided in this package are a series of functions to save animations to various formats, e.g. Flash, 'GIF', HTML pages, 'PDF' and videos. 'PDF' animations can be inserted into 'Sweave' / 'knitr' easily.

Maintained by Yihui Xie. Last updated 2 years ago.

animation statistical-computing statistical-graphics statistics

208 stars 12.13 score 2.5k scripts 28 dependents

rstudio

shinytest2:Testing for Shiny Applications

Automated unit testing of Shiny applications through a headless 'Chromium' browser.

Maintained by Barret Schloerke. Last updated 5 days ago.

cpp

108 stars 12.13 score 704 scripts 1 dependents

bioc

SeqArray:Data management of large-scale whole-genome sequence variant calls using GDS files

Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

Maintained by Xiuwen Zheng. Last updated 8 days ago.

infrastructure datarepresentation sequencing genetics bioinformatics gds-format snp snv wes wgs cpp

45 stars 12.11 score 1.1k scripts 9 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.

dataimport sequencing qualitycontrol bioconductor-package core-package zlib cpp

8 stars 12.08 score 1.8k scripts 49 dependents

ropensci

RefManageR:Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management

Provides tools for importing and working with bibliographic references. It greatly enhances the 'bibentry' class by providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references, supports 'UTF-8' encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez', 'CrossRef', and 'Zotero' are provided for importing references and references can be created from locally stored 'PDF' files using 'Poppler'. Includes functions for citing and generating a bibliography with hyperlinks for documents prepared with 'RMarkdown' or 'RHTML'.

Maintained by Mathew W. McLean. Last updated 4 months ago.

peer-reviewed

115 stars 12.06 score 2.3k scripts 16 dependents

ropensci

rotl:Interface to the 'Open Tree of Life' API

An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.

Maintained by Francois Michonneau. Last updated 2 years ago.

metadata ropensci phylogenetics independant-contrasts biodiversity peer-reviewed phylogeny taxonomy

40 stars 12.05 score 356 scripts 29 dependents

dreamrs

datamods:Modules to Import and Manipulate Data in 'Shiny'

'Shiny' modules to import data into an application or 'addin' from various sources, and to manipulate them after that.

Maintained by Victor Perrier. Last updated 27 days ago.

shiny shiny-modules

144 stars 12.03 score 174 scripts 7 dependents

bioc

slingshot:Tools for ordering single-cell sequencing

Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.

Maintained by Kelly Street. Last updated 5 months ago.

clustering differentialexpression geneexpression rnaseq sequencing software singlecell transcriptomics visualization

286 stars 12.01 score 1.0k scripts 4 dependents

bioc

ExperimentHub:Client to access ExperimentHub resources

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

infrastructure dataimport gui thirdpartyclient core-package u24ca289073

10 stars 11.94 score 764 scripts 57 dependents

bioc

GenomicDataCommons:NIH / NCI Genomic Data Commons Access

Programmatically access the NIH / NCI Genomic Data Commons RESTful service.

Maintained by Sean Davis. Last updated 2 months ago.

dataimport sequencing api-client bioconductor bioinformatics cancer core-services data-science genomics nci tcga vignette

87 stars 11.94 score 238 scripts 12 dependents

jinghuazhao

gap:Genetic Analysis Package

As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

Maintained by Jing Hua Zhao. Last updated 7 days ago.

genetics imputation lmm fortran

12 stars 11.94 score 448 scripts 16 dependents

pecanproject

PEcAn.DB:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by David LeBauer. Last updated 20 hours ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

216 stars 11.91 score 127 scripts 27 dependents

bioc

QFeatures:Quantitative features for mass spectrometry data

The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.

Maintained by Laurent Gatto. Last updated 28 days ago.

infrastructure massspectrometry proteomics metabolomics bioconductor mass-spectrometry

27 stars 11.87 score 278 scripts 49 dependents

guangchuangyu

hexSticker:Create Hexagon Sticker in R

Helper functions for creating reproducible hexagon sticker purely in R.

Maintained by Guangchuang Yu. Last updated 2 months ago.

ggplot2 hexagon-sticker logo stickers visualization

773 stars 11.79 score 1.3k scripts 8 dependents

bioc

methylKit:DNA methylation analysis from high-throughput bisulfite sequencing results

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.

Maintained by Altuna Akalin. Last updated 1 months ago.

dnamethylation sequencing methylseq genome-biology methylation statistical-analysis visualization curl bzip2 xz-utils zlib cpp

224 stars 11.78 score 578 scripts 3 dependents

r-causal

ggdag:Analyze and Create Elegant Directed Acyclic Graphs

Tidy, analyze, and plot directed acyclic graphs (DAGs). 'ggdag' is built on top of 'dagitty', an R package that uses the 'DAGitty' web tool (<https://dagitty.net/>) for creating and analyzing DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using 'ggplot2' and 'ggraph', as well as common analytic and graphical functions, such as determining adjustment sets and node relationships.

Maintained by Malcolm Barrett. Last updated 8 months ago.

causal-inference dag ggplot-extension

443 stars 11.78 score 1.8k scripts 5 dependents

jessecambon

tidygeocoder:Geocoding Made Easy

An intuitive interface for getting data from geocoding services.

Maintained by Jesse Cambon. Last updated 4 hours ago.

geocoding rspatial tidyverse

288 stars 11.67 score 1.0k scripts 10 dependents

wilkelab

gridtext:Improved Text Rendering Support for 'Grid' Graphics

Provides support for rendering of formatted text using 'grid' graphics. Text can be formatted via a minimal subset of 'Markdown', 'HTML', and inline 'CSS' directives, and it can be rendered both with and without word wrap.

Maintained by Brenton M. Wiernik. Last updated 1 years ago.

cpp

96 stars 11.66 score 344 scripts 208 dependents

jthomasmock

gtExtras:Extending 'gt' for Beautiful HTML Tables

Provides additional functions for creating beautiful tables with 'gt'. The functions are generally wrappers around boilerplate or adding opinionated niche capabilities and helpers functions.

Maintained by Thomas Mock. Last updated 12 months ago.

data-science data-visualization datascience ggplot2 gt plots sparkline sparkline-graphs sparklines tables

201 stars 11.66 score 2.4k scripts 5 dependents

mrkaye97

slackr:Send Messages, Images, R Objects and Files to 'Slack' Channels/Users

'Slack' <https://slack.com/> provides a service for teams to collaborate by sharing messages, images, links, files and more. Functions are provided that make it possible to interact with the 'Slack' platform 'API'. When you need to share information or data from R, rather than resort to copy/ paste in e-mails or other services like 'Skype' <https://www.skype.com/en/>, you can use this package to send well-formatted output from multiple R objects and expressions to all teammates at the same time with little effort. You can also send images from the current graphics device, R objects, and upload files.

Maintained by Matt Kaye. Last updated 6 months ago.

slack

306 stars 11.66 score 179 scripts

ateucher

rmapshaper:Client for 'mapshaper' for 'Geospatial' Operations

Edit and simplify 'geojson', 'Spatial', and 'sf' objects. This is wrapper around the 'mapshaper' 'JavaScript' library by Matthew Bloch <https://github.com/mbloch/mapshaper/> to perform topologically-aware polygon simplification, as well as other operations such as clipping, erasing, dissolving, and converting 'multi-part' to 'single-part' geometries.

Maintained by Andy Teucher. Last updated 9 months ago.

rlang

204 stars 11.64 score 2.1k scripts 18 dependents

haleyjeppson

ggmosaic:Mosaic Plots in the 'ggplot2' Framework

Mosaic plots in the 'ggplot2' framework. Mosaic plot functionality is provided in a single 'ggplot2' layer by calling the geom 'mosaic'.

Maintained by Haley Jeppson. Last updated 6 months ago.

167 stars 11.63 score 1.8k scripts 4 dependents

pecanproject

PEcAn.data.atmosphere:PEcAn Functions Used for Managing Climate Driver Data

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The PECAn.data.atmosphere package converts climate driver data into a standard format for models integrated into PEcAn. As a standalone package, it provides an interface to access diverse climate data sets.

Maintained by David LeBauer. Last updated 20 hours ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

216 stars 11.63 score 64 scripts 14 dependents

bioc

bumphunter:Bump Hunter

Tools for finding bumps in genomic data

Maintained by Tamilselvi Guharaj. Last updated 5 months ago.

dnamethylation epigenetics infrastructure multiplecomparison immunooncology

16 stars 11.61 score 210 scripts 43 dependents

robjhyndman

tsfeatures:Time Series Feature Extraction

Methods for extracting various features from time series data. The features provided are those from Hyndman, Wang and Laptev (2013) <doi:10.1109/ICDMW.2015.104>, Kang, Hyndman and Smith-Miles (2017) <doi:10.1016/j.ijforecast.2016.09.004> and from Fulcher, Little and Jones (2013) <doi:10.1098/rsif.2013.0048>. Features include spectral entropy, autocorrelations, measures of the strength of seasonality and trend, and so on. Users can also define their own feature functions.

Maintained by Rob Hyndman. Last updated 8 months ago.

feature-extraction time-series

257 stars 11.55 score 268 scripts 22 dependents

workflowr

workflowr:A Framework for Reproducible and Collaborative Data Science

Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results.

Maintained by John Blischak. Last updated 4 months ago.

git project-management rmarkdown website workflow

848 stars 11.53 score 566 scripts

urbananalyst

dodgr:Distances on Directed Graphs

Distances on dual-weighted directed graphs using priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>). Weighted directed graphs have weights from A to B which may differ from those from B to A. Dual-weighted directed graphs have two sets of such weights. A canonical example is a street network to be used for routing in which routes are calculated by weighting distances according to the type of way and mode of transport, yet lengths of routes must be calculated from direct distances.

Maintained by Mark Padgham. Last updated 3 days ago.

distance openstreetmap router shortest-paths street-networks cpp

129 stars 11.52 score 229 scripts 4 dependents

bioc

systemPipeR:systemPipeR: Workflow Environment for Data Analysis and Report Generation

systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.

Maintained by Thomas Girke. Last updated 5 months ago.

genetics infrastructure dataimport sequencing rnaseq riboseq chipseq methylseq snp geneexpression coverage genesetenrichment alignment qualitycontrol immunooncology reportwriting workflowstep workflowmanagement

53 stars 11.52 score 344 scripts 3 dependents

bioc

mia:Microbiome analysis

mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.

Maintained by Tuomas Borman. Last updated 5 days ago.

microbiome software dataimport analysis bioconductor cpp

51 stars 11.51 score 316 scripts 5 dependents

r-lib

gmailr:Access the 'Gmail' 'RESTful' API

An interface to the 'Gmail' 'RESTful' API. Allows access to your 'Gmail' messages, threads, drafts and labels.

Maintained by Jennifer Bryan. Last updated 1 years ago.

230 stars 11.50 score 289 scripts 1 dependents

ropensci

rredlist:'IUCN' Red List Client

'IUCN' Red List (<https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.

Maintained by William Gearty. Last updated 2 months ago.

iucn biodiversity api web-services traits habitat species conservation api-wrapper iucn-red-list taxize

53 stars 11.49 score 195 scripts 24 dependents

bioc

msa:Multiple Sequence Alignment

The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.

Maintained by Ulrich Bodenhofer. Last updated 2 months ago.

multiplesequencealignment alignment multiplecomparison sequencing cpp

17 stars 11.46 score 744 scripts 6 dependents

bioc

destiny:Creates diffusion maps

Create and plot diffusion maps.

Maintained by Philipp Angerer. Last updated 4 months ago.

cellbiology cellbasedassays clustering software visualization diffusion-maps dimensionality-reduction cpp

82 stars 11.44 score 792 scripts 1 dependents

bioc

annotate:Annotation for microarrays

Using R enviroments for annotation.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotation pathways go

11.41 score 812 scripts 239 dependents

bioc

VariantAnnotation:Annotation of Genetic Variants

Annotate variants, compute amino acid coding changes, predict coding outcomes.

Maintained by Bioconductor Package Maintainer. Last updated 3 months ago.

dataimport sequencing snp annotation genetics variantannotation curl bzip2 xz-utils zlib

11.39 score 1.9k scripts 152 dependents

bioc

PharmacoGx:Analysis of Large-Scale Pharmacogenomic Data

Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.

Maintained by Benjamin Haibe-Kains. Last updated 3 months ago.

geneexpression pharmacogenetics pharmacogenomics software classification datasets pharmacogenomic pharmacogx cpp

68 stars 11.39 score 442 scripts 3 dependents

r4ss

r4ss:R Code for Stock Synthesis

A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.23.1, from December 2024). Support for 3.24 models is only through the core functions for reading output and plotting.

Maintained by Ian G. Taylor. Last updated 20 days ago.

fisheries fisheries-stock-assessment stock-synthesis

43 stars 11.38 score 1.0k scripts 2 dependents

doi-usgs

nhdplusTools:NHDPlus Tools

Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.

Maintained by David Blodgett. Last updated 1 months ago.

87 stars 11.38 score 348 scripts 5 dependents

bioc

pathview:a tool set for pathway based data integration and visualization

Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

Maintained by Weijun Luo. Last updated 3 days ago.

pathways graphandnetwork visualization genesetenrichment differentialexpression geneexpression microarray rnaseq genetics metabolomics proteomics systemsbiology sequencing

40 stars 11.37 score 1.6k scripts 10 dependents

rolkra

explore:Simplifies Exploratory Data Analysis

Interactive data exploration with one line of code, automated reporting or use an easy to remember set of tidy functions for low code exploratory data analysis.

Maintained by Roland Krasser. Last updated 1 days ago.

data-exploration data-visualisation decision-trees eda rmarkdown shiny tidy

230 stars 11.36 score 221 scripts 1 dependents

ropensci

biomartr:Genomic Data Retrieval

Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.

Maintained by Hajk-Georg Drost. Last updated 2 months ago.

biomart genomic-data-retrieval annotation-retrieval database-retrieval ncbi ensembl biological-data-retrieval ensembl-servers genome genome-annotation genome-retrieval genomics meta-analysis metagenomics ncbi-genbank peer-reviewed proteome sequenced-genomes

218 stars 11.35 score 129 scripts 3 dependents

dsy109

mixtools:Tools for Analyzing Finite Mixture Models

Analyzes finite mixture models for various parametric and semiparametric settings. This includes mixtures of parametric distributions (normal, multivariate normal, multinomial, gamma), various Reliability Mixture Models (RMMs), mixtures-of-regressions settings (linear regression, logistic regression, Poisson regression, linear regression with changepoints, predictor-dependent mixing proportions, random effects regressions, hierarchical mixtures-of-experts), and tools for selecting the number of components (bootstrapping the likelihood ratio test statistic, mixturegrams, and model selection criteria). Bayesian estimation of mixtures-of-linear-regressions models is available as well as a novel data depth method for obtaining credible bands. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772 and the Chan Zuckerberg Initiative: Essential Open Source Software for Science (Grant No. 2020-255193).

Maintained by Derek Young. Last updated 10 months ago.

mixture-models mixture-of-experts semiparametric-regression

20 stars 11.34 score 1.4k scripts 56 dependents

r-hub

rhub:Tools for R Package Developers

R-hub v2 uses GitHub Actions to run 'R CMD check' and similar package checks. The 'rhub' package helps you set up R-hub v2 for your R package, and start running checks.

Maintained by Gábor Csárdi. Last updated 25 days ago.

359 stars 11.33 score 191 scripts 1 dependents

ropensci

ssh:Secure Shell (SSH) Client for R

Connect to a remote server over SSH to transfer files via SCP, setup a secure tunnel, or run a command or script on the host while streaming stdout and stderr directly to the client.

Maintained by Jeroen Ooms. Last updated 5 days ago.

libssh ssh ssh-client

129 stars 11.33 score 128 scripts 10 dependents

kurthornik

tseries:Time Series Analysis and Computational Finance

Time series analysis and computational finance.

Maintained by Kurt Hornik. Last updated 6 months ago.

fortran openblas

4 stars 11.29 score 10k scripts 289 dependents

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 3 days ago.

analytics bioinformatics chart charting dash dashboard data-analytics data-science data-visualization genomics graphs javascript network network-visualization python reproducible-research shiny visualization

297 stars 11.28 score 145 scripts

bioc

MAST:Model-based Analysis of Single Cell Transcriptomics

Methods and models for handling zero-inflated single cell assay data.

Maintained by Andrew McDavid. Last updated 5 months ago.

geneexpression differentialexpression genesetenrichment rnaseq transcriptomics singlecell

232 stars 11.28 score 1.8k scripts 5 dependents

mrcieu

TwoSampleMR:Two Sample MR Functions and Interface to MRC Integrative Epidemiology Unit OpenGWAS Database

A package for performing Mendelian randomization using GWAS summary data. It uses the IEU OpenGWAS database <https://gwas.mrcieu.ac.uk/> to automatically obtain data, and a wide range of methods to run the analysis.

Maintained by Gibran Hemani. Last updated 4 days ago.

476 stars 11.27 score 1.7k scripts 1 dependents

azure

Microsoft365R:Interface to the 'Microsoft 365' Suite of Cloud Services

An interface to the 'Microsoft 365' (formerly known as 'Office 365') suite of cloud services, building on the framework supplied by the 'AzureGraph' package. Enables access from R to data stored in 'Teams', 'SharePoint Online' and 'OneDrive', including the ability to list drive folder contents, upload and download files, send messages, and retrieve data lists. Also provides a full-featured 'Outlook' email client, with the ability to send emails and manage emails and mail folders.

Maintained by Hong Ooi. Last updated 30 days ago.

azure-sdk-r microsoft-365 microsoft-graph-api office-365 onedrive onedrive-for-business sharepoint-online

329 stars 11.26 score 88 scripts 8 dependents

bioc

zellkonverter:Conversion Between scRNA-seq Objects

Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk.

Maintained by Luke Zappia. Last updated 23 days ago.

singlecell dataimport datarepresentation bioconductor conversion scrna-seq

159 stars 11.25 score 660 scripts 4 dependents

paws-r

paws:Amazon Web Services Software Development Kit

Interface to Amazon Web Services <https://aws.amazon.com>, including storage, database, and compute services, such as 'Simple Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda' functions-as-a-service.

Maintained by Dyfan Jones. Last updated 19 days ago.

aws aws-sdk

332 stars 11.25 score 177 scripts 12 dependents

adeverse

adespatial:Multivariate Multiscale Spatial Analysis

Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.

Maintained by Aurélie Siberchicot. Last updated 9 hours ago.

fortran openblas

36 stars 11.25 score 398 scripts 2 dependents

bioc

karyoploteR:Plot customizable linear genomes displaying arbitrary data

karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

Maintained by Bernat Gel. Last updated 5 months ago.

visualization copynumbervariation sequencing coverage dnaseq chipseq methylseq dataimport onechannel bioconductor bioinformatics data-visualization genome genomics-visualization plotting-in-r

307 stars 11.25 score 656 scripts 4 dependents

rstudio

webshot2:Take Screenshots of Web Pages

Takes screenshots of web pages, including Shiny applications and R Markdown documents. 'webshot2' uses headless Chrome or Chromium as the browser back-end.

Maintained by Winston Chang. Last updated 2 months ago.

114 stars 11.20 score 928 scripts 17 dependents

ropensci

EML:Read and Write Ecological Metadata Language Files

Work with Ecological Metadata Language ('EML') files. 'EML' is a widely used metadata standard in the ecological and environmental sciences, described in Jones et al. (2006), <doi:10.1146/annurev.ecolsys.37.091305.110031>.

Maintained by Carl Boettiger. Last updated 3 years ago.

eml eml-metadata metadata-standard

97 stars 11.19 score 378 scripts 7 dependents

ncss-tech

soilDB:Soil Database Interface

A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.

Maintained by Andrew Brown. Last updated 2 hours ago.

kssl nasis nrcs soil soil-data-access soil-survey soilweb sql usda

86 stars 11.19 score 1.0k scripts 1 dependents

jamiemkass

ENMeval:Automated Tuning and Evaluations of Ecological Niche Models

Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate range overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html>.

Maintained by Jamie M. Kass. Last updated 3 days ago.

49 stars 11.16 score 332 scripts 2 dependents

bioc

genomation:Summary, annotation and visualization of genomic data

A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.

Maintained by Altuna Akalin. Last updated 5 months ago.

annotation sequencing visualization cpgisland cpp

76 stars 11.13 score 738 scripts 5 dependents

guangchuangyu

ggimage:Use Image in 'ggplot2'

Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.

Maintained by Guangchuang Yu. Last updated 1 years ago.

ggplot2 image visualization

172 stars 11.12 score 2.4k scripts 20 dependents

bioc

genefilter:genefilter: methods for filtering genes from high-throughput experiments

Some basic functions for filtering genes.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

microarray fortran cpp

11.11 score 2.4k scripts 143 dependents

usepa

elevatr:Access Elevation Data from Various APIs

Several web services are available that provide access to elevation data. This package provides access to many of those services and returns elevation data either as an 'sf' simple features object from point elevation services or as a 'raster' object from raster elevation services. In future versions, 'elevatr' will drop support for 'raster' and will instead return 'terra' objects. Currently, the package supports access to the Amazon Web Services Terrain Tiles <https://registry.opendata.aws/terrain-tiles/>, the Open Topography Global Datasets API <https://opentopography.org/developers/>, and the USGS Elevation Point Query Service <https://apps.nationalmap.gov/epqs/>.

Maintained by Jeffrey Hollister. Last updated 7 months ago.

digital-elevation-model elevation-data elevatr epa mapzen-elevation-service r-language

206 stars 11.11 score 1.3k scripts 3 dependents

fmichonneau

phylobase:Base Package for Phylogenetic Structures and Comparative Data

Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.

Maintained by Francois Michonneau. Last updated 1 years ago.

phylogenetics cpp

18 stars 11.10 score 394 scripts 18 dependents

wilkox

ggfittext:Fit Text Inside a Box in 'ggplot2'

A 'ggplot2' extension to fit text into a box by growing, shrinking or wrapping the text.

Maintained by David Wilkins. Last updated 1 years ago.

ggplot2

306 stars 11.08 score 234 scripts 33 dependents

covid19datahub

COVID19:COVID-19 Data Hub

Unified datasets for a better understanding of COVID-19.

Maintained by Emanuele Guidotti. Last updated 1 months ago.

2019-ncov coronavirus covid-19 covid-data covid19-data

252 stars 11.08 score 265 scripts

ropengov

eurostat:Tools for Eurostat Open Data

Tools to download data from the Eurostat database <https://ec.europa.eu/eurostat> together with search and manipulation utilities.

Maintained by Leo Lahti. Last updated 1 months ago.

ropengov eurostat eurostat-data

242 stars 11.07 score 892 scripts 4 dependents

bioc

scater:Single-Cell Analysis Toolkit for Gene Expression Data in R

A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.

Maintained by Alan OCallaghan. Last updated 25 days ago.

immunooncology singlecell rnaseq qualitycontrol preprocessing normalization visualization dimensionreduction transcriptomics geneexpression sequencing software dataimport datarepresentation infrastructure coverage

11.07 score 12k scripts 43 dependents

paws-r

paws.common:Paws Low-Level Amazon Web Services API

Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).

Maintained by Dyfan Jones. Last updated 19 days ago.

aws aws-sdk cpp

332 stars 11.07 score 39 dependents

ipums

ipumsr:An R Interface for Downloading, Reading, and Handling IPUMS Data

An easy way to work with census, survey, and geographic data provided by IPUMS in R. Generate and download data through the IPUMS API and load IPUMS files into R with their associated metadata to make analysis easier. IPUMS data describing 1.4 billion individuals drawn from over 750 censuses and surveys is available free of charge from the IPUMS website <https://www.ipums.org>.

Maintained by Derek Burk. Last updated 1 months ago.

30 stars 11.05 score 720 scripts 2 dependents

bioc

universalmotif:Import, Modify, and Export Motifs with R

Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.

Maintained by Benjamin Jean-Marie Tremblay. Last updated 5 months ago.

motifannotation motifdiscovery dataimport generegulation motif-analysis motif-enrichment-analysis sequence-logo cpp

28 stars 11.04 score 342 scripts 12 dependents

openml

OpenML:Open Machine Learning and Open Data Platform

We provide an R interface to 'OpenML.org' which is an online machine learning platform where researchers can access open data, download and upload data sets, share their machine learning tasks and experiments and organize them online to work and collaborate with other researchers. The R interface allows to query for data sets with specific properties, and allows the downloading and uploading of data sets, tasks, flows and runs. See <https://www.openml.org/guide/api> for more information.

Maintained by Giuseppe Casalicchio. Last updated 10 months ago.

arff benchmarking benchmarking-suite classification data-science database dataset datasets machine-learning machine-learning-algorithms open-data open-science opendata openml openscience regression reproducible-research statistics

97 stars 11.04 score 7.1k scripts

config-i1

greybox:Toolbox for Model Building and Forecasting

Implements functions and instruments for regression model building and its application to forecasting. The main scope of the package is in variables selection and models specification for cases of time series data. This includes promotional modelling, selection between different dynamic regressions with non-standard distributions of errors, selection based on cross validation, solutions to the fat regression model problem and more. Models developed in the package are tailored specifically for forecasting purposes. So as a results there are several methods that allow producing forecasts from these models and visualising them.

Maintained by Ivan Svetunkov. Last updated 17 days ago.

forecasting model-selection model-selection-and-evaluation regression regression-models statistics cpp

30 stars 11.03 score 97 scripts 34 dependents

mhahsler

arulesViz:Visualizing Association Rules and Frequent Itemsets

Extends package 'arules' with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration. Michael Hahsler (2017) <doi:10.32614/RJ-2017-047>.

Maintained by Michael Hahsler. Last updated 7 months ago.

arules association-rules frequent-itemsets interactive-visualizations visualization

54 stars 11.03 score 1.7k scripts 2 dependents

bioc

CATALYST:Cytometry dATa anALYSis Tools

CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively.

Maintained by Helena L. Crowell. Last updated 4 months ago.

clustering dataimport differentialexpression experimentaldesign flowcytometry immunooncology massspectrometry normalization preprocessing singlecell software statisticalmethod visualization

67 stars 10.99 score 362 scripts 2 dependents

pecanproject

PEcAn.utils:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Rob Kooper. Last updated 20 hours ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

216 stars 10.95 score 218 scripts 35 dependents

ropensci

CoordinateCleaner:Automated Cleaning of Occurrence Records from Biological Collections

Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.

Maintained by Alexander Zizka. Last updated 1 years ago.

82 stars 10.93 score 306 scripts 3 dependents

bioc

infercnv:Infer Copy Number Variation from Single-Cell RNA-Seq Data

Using single-cell RNA-Seq expression to visualize CNV in cells.

Maintained by Christophe Georgescu. Last updated 5 months ago.

software copynumbervariation variantdetection structuralvariation genomicvariation genetics transcriptomics statisticalmethod bayesian hiddenmarkovmodel singlecell jags cpp

601 stars 10.92 score 674 scripts

bioc

EnrichedHeatmap:Making Enriched Heatmaps

Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.

Maintained by Zuguang Gu. Last updated 5 months ago.

software visualization sequencing genomeannotation coverage cpp

190 stars 10.87 score 330 scripts 1 dependents

marce10

warbleR:Streamline Bioacoustic Analysis

Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.

Maintained by Marcelo Araya-Salas. Last updated 2 months ago.

animal-acoustic-signals audio-processing bioacoustics spectrogram streamline-analysis cpp

56 stars 10.86 score 270 scripts 4 dependents

michelnivard

gptstudio:Use Large Language Models Directly in your Development Environment

Large language models are readily accessible via API. This package lowers the barrier to use the API inside of your development environment. For more on the API, see <https://platform.openai.com/docs/introduction>.

Maintained by James Wade. Last updated 6 days ago.

chatgpt gpt-3 rstudio rstudio-addin

930 stars 10.85 score 43 scripts 1 dependents

moodymudskipper

flow:View and Browse Code Using Flow Diagrams

Visualize as flow diagrams the logic of functions, expressions or scripts in a static way or when running a call, visualize the dependencies between functions or between modules in a shiny app, and more.

Maintained by Antoine Fabri. Last updated 4 months ago.

405 stars 10.84 score 61 scripts