R-universe search: curl

jeroen

curl:A Modern and Flexible Web Client for R

Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.

Maintained by Jeroen Ooms. Last updated 8 days ago.

curl

100.5 match 222 stars 20.02 score 4.0k scripts 5.9k dependents

apache

arrow:Integration to 'Apache' 'Arrow'

'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an interface to the 'Arrow C++' library.

Maintained by Jonathan Keane. Last updated 2 months ago.

arrow curl openssl cpp

33.0 match 15k stars 19.25 score 10k scripts 82 dependents

bioc

rhdf5:R Interface to HDF5

This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

Maintained by Mike Smith. Last updated 7 days ago.

infrastructure dataimport hdf5 rhdf5 openssl curl zlib cpp

33.0 match 62 stars 15.87 score 4.2k scripts 232 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

33.0 match 28 stars 15.34 score 3.2k scripts 569 dependents

bioc

maftools:Summarize, Analyze and Visualize MAF Files

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

Maintained by Anand Mayakonda. Last updated 5 months ago.

datarepresentation dnaseq visualization drivermutation variantannotation featureextraction classification somaticmutation sequencing functionalgenomics survival bioinformatics cancer-genome-atlas cancer-genomics genomics maf-files tcga curl bzip2 xz-utils zlib

33.0 match 461 stars 14.58 score 948 scripts 18 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

33.0 match 12.66 score 6.7k scripts 480 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

33.0 match 224 stars 11.78 score 578 scripts 3 dependents

cran

RCurl:General Network (HTTP/FTP/...) Client Interface for R

A wrapper for 'libcurl' <https://curl.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.

Maintained by CRAN Team. Last updated 10 days ago.

curl

44.6 match 2 stars 8.50 score 1.0k 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

33.0 match 11.39 score 1.9k scripts 152 dependents

bioc

Rhtslib:HTSlib high-throughput sequencing library as an R package

This package provides version 1.18 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").

Maintained by Hervé Pagès. Last updated 27 days ago.

dataimport sequencing bioconductor-package core-package curl bzip2 xz-utils zlib

33.0 match 11 stars 11.25 score 3 scripts 591 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

25.5 match 107 stars 14.07 score 240 scripts 168 dependents

bioc

scPipe:Pipeline for single cell multi-omic data pre-processing

A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.

Maintained by Shian Su. Last updated 4 months ago.

immunooncology software sequencing rnaseq geneexpression singlecell visualization sequencematching preprocessing qualitycontrol genomeannotation dataimport curl bzip2 xz-utils zlib cpp

33.0 match 68 stars 9.02 score 84 scripts

bioc

bamsignals:Extract read count signals from bam files

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

Maintained by Johannes Helmuth. Last updated 5 months ago.

dataimport sequencing coverage alignment curl bzip2 xz-utils zlib cpp

33.0 match 15 stars 8.95 score 31 scripts 11 dependents

bioc

QuasR:Quantify and Annotate Short Reads in R

This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest. Read alignments are either generated through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments that require spliced alignments), or can be provided in the form of bam files.

Maintained by Michael Stadler. Last updated 1 months ago.

genetics preprocessing sequencing chipseq rnaseq methylseq coverage alignment qualitycontrol immunooncology curl bzip2 xz-utils zlib cpp

33.0 match 6 stars 8.63 score 79 scripts 1 dependents

bioc

csaw:ChIP-Seq Analysis with Windows

Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

Maintained by Aaron Lun. Last updated 2 months ago.

multiplecomparison chipseq normalization sequencing coverage genetics annotation differentialpeakcalling curl bzip2 xz-utils zlib cpp

33.0 match 8.32 score 498 scripts 7 dependents

aidenlab

strawr:Fast Implementation of Reading/Dump for .hic Files

API for fast data extraction for .hic files that provides programmatic access to the matrices. It doesn't store the pointer data for all the matrices, only the one queried, and currently we are only supporting matrices (not vectors).

Maintained by Neva Cherniavsky Durand. Last updated 1 years ago.

curl zlib cpp

33.0 match 67 stars 8.23 score 49 scripts 11 dependents

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

13.0 match 989 stars 20.56 score 29k scripts 4.3k dependents

bioc

FLAMES:FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.

Maintained by Changqing Wang. Last updated 19 hours ago.

rnaseq singlecell transcriptomics dataimport differentialsplicing alternativesplicing geneexpression longread zlib curl bzip2 xz-utils cpp

33.0 match 33 stars 8.04 score 12 scripts

bioc

DiffBind:Differential Binding Analysis of ChIP-Seq Peak Data

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Maintained by Rory Stark. Last updated 2 months ago.

sequencing chipseq atacseq dnaseseq methylseq ripseq differentialpeakcalling differentialmethylation generegulation histonemodification peakdetection biomedicalinformatics cellbiology multiplecomparison normalization reportwriting epigenetics functionalgenomics curl bzip2 xz-utils zlib cpp

33.0 match 7.13 score 512 scripts 2 dependents

bioc

h5mread:A fast HDF5 reader

The main function in the h5mread package is h5mread(), which allows reading arbitrary data from an HDF5 dataset into R, similarly to what the h5read() function from the rhdf5 package does. In the case of h5mread(), the implementation has been optimized to make it as fast and memory-efficient as possible.

Maintained by Hervé Pagès. Last updated 2 months ago.

infrastructure datarepresentation dataimport openssl curl zlib

33.0 match 1 stars 6.98 score 4 scripts 127 dependents

zilong-li

vcfppR:Rapid Manipulation of the Variant Call Format (VCF)

The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.

Maintained by Zilong Li. Last updated 16 hours ago.

bioinformatics fastr htslib population-genetics population-genomics vcf vcf-data visulization libdeflate zlib bzip2 xz-utils curl cpp

33.0 match 13 stars 6.72 score 16 scripts

bioc

deepSNV:Detection of subclonal SNVs in deep sequencing data.

This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.

Maintained by Moritz Gerstung. Last updated 5 months ago.

geneticvariability snp sequencing genetics dataimport curl bzip2 xz-utils zlib cpp

33.0 match 6.53 score 38 scripts 1 dependents

eguidotti

calculus:High Dimensional Numerical and Symbolic Calculus

Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2022) <doi:10.18637/jss.v104.i05>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.

Maintained by Emanuele Guidotti. Last updated 2 years ago.

calculus coordinate-systems curl divergence einstein finite-difference gradient hermite hessian jacobian laplacian numerical-derivation numerical-derivatives numerical-differentiation symbolic-computation symbolic-differentiation taylor cpp

22.0 match 47 stars 8.98 score 66 scripts 7 dependents

bioc

epialleleR:Fast, Epiallele-Aware Methylation Caller and Reporter

Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract and visualise methylation patterns and assess allele specificity of methylation.

Maintained by Oleksii Nikolaienko. Last updated 26 days ago.

dnamethylation epigenetics methylseq longread bioconductor dna-methylation epiallele next-generation-sequencing samtools curl bzip2 xz-utils zlib cpp

33.0 match 4 stars 5.94 score 5 scripts

bioc

raer:RNA editing tools in R

Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.

Maintained by Kent Riemondy. Last updated 5 months ago.

multiplecomparison rnaseq singlecell sequencing coverage epitranscriptomics featureextraction annotation alignment bioconductor-package rna-seq-analysis single-cell-analysis single-cell-rna-seq curl bzip2 xz-utils zlib

33.0 match 8 stars 5.81 score 6 scripts

bioc

diffHic:Differential Analysis of Hi-C Data

Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.

Maintained by Aaron Lun. Last updated 4 months ago.

multiplecomparison preprocessing sequencing coverage alignment normalization clustering hic curl bzip2 xz-utils zlib cpp

33.0 match 5.58 score 38 scripts

lucasnell

jackalope:A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator

Simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina <https://www.illumina.com/> and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. 'jackalope' can simulate single, paired-end, or mate-pair Illumina reads, as well as PacBio reads. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/polymerase chain reaction (PCR) duplicates. Simulating Illumina sequencing is based on ART by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>. PacBio sequencing simulation is based on SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>. All outputs can be written to standard file formats.

Maintained by Lucas A. Nell. Last updated 1 years ago.

zlib openblas curl bzip2 xz-utils cpp

33.0 match 8 stars 5.28 score 24 scripts

bioc

podkat:Position-Dependent Kernel Association Test

This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.

Maintained by Ulrich Bodenhofer. Last updated 5 months ago.

genetics wholegenome annotation variantannotation sequencing dataimport curl bzip2 xz-utils zlib cpp

33.0 match 5.02 score 6 scripts

bioc

h5vc:Managing alignment tallies using a hdf5 backend

This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.

Maintained by Paul Theodor Pyl. Last updated 2 months ago.

curl bzip2 xz-utils zlib cpp

33.0 match 4.48 score 2 scripts

bioc

mitoClone2:Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.

Maintained by Benjamin Story. Last updated 5 months ago.

annotation dataimport genetics snp software singlecell alignment curl bzip2 xz-utils zlib cpp

33.0 match 1 stars 4.48 score 9 scripts

sckott

request:High Level 'HTTP' Client

High level and easy 'HTTP' client for 'R' that makes assumptions that should work in most cases. Provides functions for building 'HTTP' queries, including query parameters, body requests, headers, authentication, and more.

Maintained by Scott Chamberlain. Last updated 5 years ago.

api curl curl-library http

20.8 match 36 stars 6.16 score 812 scripts

ropensci

vcr:Record 'HTTP' Calls to Disk

Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.

Maintained by Scott Chamberlain. Last updated 27 days ago.

http https api web-services curl mock mocking http-mocking testing testing-tools tdd unit-testing vcr

11.0 match 77 stars 10.06 score 165 scripts

sckott

fauxpas:HTTP Error Helpers

HTTP error helpers. Methods included for general purpose HTTP error handling, as well as individual methods for every HTTP status code, both via status code numbers as well as their descriptive names. Supports ability to adjust behavior to stop, message or warning. Includes ability to use custom whisker template to have any configuration of status code, short description, and verbose message. Currently supports integration with 'crul', 'curl', and 'httr'.

Maintained by Scott Chamberlain. Last updated 1 years ago.

http https api web-services curl errors error error-handling

13.7 match 14 stars 7.97 score 36 scripts 24 dependents

dankelley

oce:Analysis of Oceanographic Data

Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.

Maintained by Dan Kelley. Last updated 4 days ago.

oceanography fortran cpp

6.7 match 146 stars 15.34 score 4.2k scripts 18 dependents

ropensci

webmockr:Stubbing and Setting Expectations on 'HTTP' Requests

Stubbing and setting expectations on 'HTTP' requests. Includes tools for stubbing 'HTTP' requests, including expected request conditions and response conditions. Match on 'HTTP' method, query parameters, request body, headers and more. Can be used for unit tests or outside of a testing context.

Maintained by Scott Chamberlain. Last updated 2 months ago.

http https api web-services curl mock mocking fakeweb http-mocking testing testing-tools tdd http-mock

11.0 match 49 stars 8.29 score 141 scripts 1 dependents

ropensci

ghql:General Purpose 'GraphQL' Client

A 'GraphQL' client, with an R6 interface for initializing a connection to a 'GraphQL' instance, and methods for constructing queries, including fragments and parameterized queries. Queries are checked with the 'libgraphqlparser' C++ parser via the 'graphql' package.

Maintained by Mark Padgham. Last updated 2 years ago.

http api web-services curl data graphql graphql-api graphql-client

11.0 match 148 stars 8.12 score 111 scripts 5 dependents

bioc

TransView:Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

This package provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.

Maintained by Julius Muller. Last updated 2 months ago.

immunooncology dnamethylation geneexpression transcription microarray sequencing chipseq rnaseq methylseq dataimport visualization clustering multiplecomparison curl bzip2 xz-utils zlib

33.0 match 2.60 score

robinhankin

hyper2:The Hyperdirichlet Distribution, Mark 2

A suite of routines for the hyperdirichlet distribution and reified Bradley-Terry; supersedes the 'hyperdirichlet' package; uses 'disordR' discipline <doi:10.48550/ARXIV.2210.03856>. To cite in publications please use Hankin 2017 <doi:10.32614/rj-2017-061>, and for Generalized Plackett-Luce likelihoods use Hankin 2024 <doi:10.18637/jss.v109.i08>.

Maintained by Robin K. S. Hankin. Last updated 3 days ago.

cpp

10.8 match 5 stars 7.91 score 38 scripts 1 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

3.7 match 246 stars 17.64 score 1.9k scripts 1.1k dependents

carlganz

docuSignr:Connect to 'DocuSign' API

Connect to the 'DocuSign' Rest API <https://www.docusign.com/p/RESTAPIGuide/RESTAPIGuide.htm>, which supports embedded signing, and sending of documents.

Maintained by Carl Ganz. Last updated 6 years ago.

curl docusign httr

11.0 match 5 stars 3.40 score 10 scripts

yihui

xfun:Supporting Functions for Packages Maintained by 'Yihui Xie'

Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.

Maintained by Yihui Xie. Last updated 14 days ago.

1.8 match 146 stars 18.19 score 916 scripts 4.4k dependents

jeroen

openssl:Toolkit for Encryption, Signatures and Certificates Based on OpenSSL

Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.

Maintained by Jeroen Ooms. Last updated 2 months ago.

openssl

1.8 match 65 stars 18.00 score 632 scripts 5.0k dependents

r-lib

pak:Another Approach to Package Installation

The goal of 'pak' is to make package installation faster and more reliable. In particular, it performs all HTTP operations in parallel, so metadata resolution and package downloads are fast. Metadata and package files are cached on the local disk as well. 'pak' has a dependency solver, so it finds version conflicts before performing the installation. This version of 'pak' supports CRAN, 'Bioconductor' and 'GitHub' packages as well.

Maintained by Gábor Csárdi. Last updated 6 days ago.

2.3 match 717 stars 13.03 score 277 scripts 17 dependents

r-lib

processx:Execute and Control System Processes

Tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes. It can read the standard output and error of the processes, using non-blocking connections. 'processx' can poll a process for standard output or error, with a timeout. It can also poll several processes at once.

Maintained by Gábor Csárdi. Last updated 1 months ago.

1.7 match 236 stars 15.52 score 340 scripts 1.4k dependents

kwstat

pals:Color Palettes, Colormaps, and Tools to Evaluate Them

A comprehensive collection of color palettes, colormaps, and tools to evaluate them. See Kovesi (2015) <doi:10.48550/arXiv.1509.03700>.

Maintained by Kevin Wright. Last updated 24 days ago.

2.3 match 83 stars 11.39 score 2.1k scripts 8 dependents

frbcesab

zenodor:Download Files from a Zenodo Repository

Lists and downloads available files of a Zenodo repository. For restricted repository a token must be provided.

Maintained by Nicolas Casajus. Last updated 2 years ago.

curl zenodo

11.0 match 3 stars 2.18 score

dataoneorg

dataone:R Interface to the DataONE REST API

Provides read and write access to data and metadata from the DataONE network <https://www.dataone.org> of data repositories. Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository. Users can also insert and update data objects on repositories that support these methods.

Maintained by Matthew B. Jones. Last updated 3 years ago.

2.3 match 36 stars 9.93 score 472 scripts 3 dependents

vubiostat

redcapAPI:Interface to 'REDCap'

Access data stored in 'REDCap' databases using the Application Programming Interface (API). 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>, Harris, et al. (2009) <doi:10.1016/j.jbi.2008.08.010>, Harris, et al. (2019) <doi:10.1016/j.jbi.2019.103208>) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The API allows users to access data and project meta data (such as the data dictionary) from the web programmatically. The 'redcapAPI' package facilitates the process of accessing data with options to prepare an analysis-ready data set consistent with the definitions in a database's data dictionary.

Maintained by Shawn Garbett. Last updated 24 days ago.

1.8 match 22 stars 10.47 score 134 scripts 2 dependents

thomasp85

ambient:A Generator of Multidimensional Noise

Generation of natural looking noise has many application within simulation, procedural generation, and art, to name a few. The 'ambient' package provides an interface to the 'FastNoise' C++ library and allows for efficient generation of perlin, simplex, worley, cubic, value, and white noise with optional perturbation in either 2, 3, or 4 (in case of simplex and white noise) dimensions.

Maintained by Thomas Lin Pedersen. Last updated 3 years ago.

cpp

2.0 match 97 stars 8.09 score 956 scripts 2 dependents

sherrillmix

taxonomizr:Functions to Work with NCBI Accessions and Taxonomy

Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.

Maintained by Scott Sherrill-Mix. Last updated 19 days ago.

1.7 match 72 stars 8.85 score 255 scripts 2 dependents

cnathe

Rlabkey:Data Exchange Between R and 'LabKey' Server

The 'LabKey' client library for R makes it easy for R users to load live data from a 'LabKey' Server, <https://www.labkey.com/>, into the R environment for analysis, provided users have permissions to read the data. It also enables R users to insert, update, and delete records stored on a 'LabKey' Server, provided they have appropriate permissions to do so.

Maintained by Cory Nathe. Last updated 18 days ago.

cpp

3.4 match 4.25 score 388 scripts 1 dependents

sportsdataverse

sportyR:Plot Scaled 'ggplot' Representations of Sports Playing Surfaces

Create scaled 'ggplot' representations of playing surfaces. Playing surfaces are drawn pursuant to rule-book specifications. This package should be used as a baseline plot for displaying any type of tracking data.

Maintained by Ross Drucker. Last updated 2 months ago.

football ggplot2 playing-surfaces sport sports-analytics sports-data sports-tracking-data sportsdataverse visualization

1.7 match 104 stars 8.08 score 97 scripts

bart1

move2:Processing and Analysing Animal Trajectories

Tools to handle, manipulate and explore trajectory data, with an emphasis on data from tracked animals. The package is designed to support large studies with several million location records and keep track of units where possible. Data import directly from 'movebank' <https://www.movebank.org/cms/movebank-main> and files is facilitated.

Maintained by Bart Kranstauber. Last updated 2 months ago.

1.8 match 7.51 score 169 scripts 1 dependents

bioc

glmSparseNet:Network Centrality Metrics for Elastic-Net Regularized Models

glmSparseNet is an R-package that generalizes sparse regression models when the features (e.g. genes) have a graph structure (e.g. protein-protein interactions), by including network-based regularizers. glmSparseNet uses the glmnet R-package, by including centrality measures of the network as penalty weights in the regularization. The current version implements regularization based on node degree, i.e. the strength and/or number of its associated edges, either by promoting hubs in the solution or orphan genes in the solution. All the glmnet distribution families are supported, namely "gaussian", "poisson", "binomial", "multinomial", "cox", and "mgaussian".

Maintained by André Veríssimo. Last updated 5 months ago.

software statisticalmethod dimensionreduction regression classification survival network graphandnetwork

1.7 match 6 stars 7.42 score 41 scripts 1 dependents

emilyriederer

projmgr:Task Tracking and Project Management with GitHub

Provides programmatic access to 'GitHub' API with a focus on project management. Key functionality includes setting up issues and milestones from R objects or 'YAML' configurations, querying outstanding or completed tasks, and generating progress updates in tables, charts, and RMarkdown reports. Useful for those using 'GitHub' in personal, professional, or academic settings with an emphasis on streamlining the workflow of data analysis projects.

Maintained by Emily Riederer. Last updated 1 years ago.

github-api project-management

1.7 match 124 stars 6.81 score 34 scripts 5 dependents

bioc

sosta:A package for the analysis of anatomical tissue structures in spatial omics data

sosta (Spatial Omics STructure Analysis) is a package for analyzing spatial omics data to explore tissue organization at the anatomical structure level. It reconstructs morphologically relevant structures based on molecular features or cell types. It further calculates a range of structural and shape metrics to quantitatively describe tissue architecture. The package is designed to integrate with other packages for the analysis of spatial (omics) data.

Maintained by Samuel Gunz. Last updated 10 days ago.

software spatial transcriptomics visualization

2.0 match 1 stars 5.68 score 2 scripts 1 dependents

banboo-data

r4googleads:'Google Ads API' Interface

Interface for the 'Google Ads API'. 'Google Ads' is an online advertising service that enables advertisers to display advertising to web users (see <https://developers.google.com/google-ads/> for more information).

Maintained by Johannes Burkhardt. Last updated 3 years ago.

google-ads-api marketing-analytics marketing-automation

2.0 match 5 stars 4.88 score 6 scripts

mrcieu

epigraphdb:Interface Package for the 'EpiGraphDB' Platform

The interface package to access data from the 'EpiGraphDB' <https://epigraphdb.org> platform. It provides easy access to the 'EpiGraphDB' platform with functions that query the corresponding REST endpoints on the API <https://api.epigraphdb.org> and return the response data in the 'tibble' data frame format.

Maintained by Yi Liu. Last updated 3 years ago.

api-client bioinformatics epidemiology graph-database mendelian-randomization phenotypes

1.5 match 27 stars 6.02 score 13 scripts

patzaw

neo2R:Neo4j to R

The aim of neo2R is to provide simple and low level connectors for querying neo4j graph databases (<https://neo4j.com/>). The objects returned by the query functions are either lists or data.frames with very little post-processing. It allows fast processing of queries returning many records. And it let the users handle post-processing according to the data model and their needs.

Maintained by Patrice Godard. Last updated 7 months ago.

1.8 match 11 stars 4.22 score 6 scripts 1 dependents

jbgruber

cookiemonster:Your Friendly Solution to Managing Browser Cookies

A convenient tool to store and format browser cookies and use them in 'HTTP' requests (for example, through 'httr2', 'httr' or 'curl').

Maintained by Johannes B. Gruber. Last updated 6 months ago.

1.8 match 1 stars 3.93 score 17 scripts

cole-johanson

smartsheetr:Access and Write 'Smartsheet' Data using the 'Smartsheet' API 2.0

Interact with the 'Smartsheet' platform through the 'Smartsheet' API 2.0. <https://smartsheet.redoc.ly/>. API is an acronym for application programming interface; the 'Smartsheet' API allows users to interact with 'Smartsheet' sheets directly within R.

Maintained by Cole Johanson. Last updated 1 years ago.

1.8 match 5 stars 3.40 score 2 scripts

olafmersmann

sendmailR:Send Email Using R

Package contains a simple SMTP client with minimal dependencies which provides a portable solution for sending email, including file attachments and inline html reports, from within R. SMTP Authentication and SSL/STARTTLS is implemented using curl.

Maintained by Olaf Mersmann. Last updated 2 years ago.

0.5 match 15 stars 9.21 score 252 scripts 4 dependents

cran

EngrExpt:Data sets from "Introductory Statistics for Engineering Experimentation"

Datasets from Nelson, Coffin and Copeland "Introductory Statistics for Engineering Experimentation" (Elsevier, 2003) with sample code.

Maintained by Douglas Bates. Last updated 16 years ago.

4.5 match 1.00 score

s915

rdbnomics:Download DBnomics Data

R access to hundreds of millions data series from DBnomics API (<https://db.nomics.world/>).

Maintained by Sebastien Galais. Last updated 4 years ago.

1.2 match 1 stars 3.77 score 118 scripts

appelmar

gdalcubes:Earth Observation Data Cubes from Satellite Image Collections

Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.

Maintained by Marius Appel. Last updated 12 days ago.

remote-sensing satellite-imagery spatial-analysis gdal netcdf cpp

0.5 match 124 stars 8.12 score 356 scripts

giocomai

plausibler:Access Plausible Analytics API

Access Plausible Analytics API.

Maintained by Giorgio Comai. Last updated 19 days ago.

api-wrapper plausible-analytics

1.7 match 5 stars 2.40 score

serkor1

cryptoQuotes:Open Access to Cryptocurrency Market Data, Sentiment Indicators and Interactive Charts

This high-level API client provides open access to cryptocurrency market data, sentiment indicators, and interactive charting tools. The data is sourced from major cryptocurrency exchanges via 'curl' and returned in 'xts'-format. The data comes in open, high, low, and close (OHLC) format with flexible granularity, ranging from seconds to months. This flexibility makes it ideal for developing and backtesting trading strategies or conducting detailed market analysis.

Maintained by Serkan Korkmaz. Last updated 5 months ago.

binance binance-api bitmart bybit bybit-api cryptocurrencies cryptocurrency cryptocurrency-exchanges huobi huobi-api kraken-api kraken-exchange-api kucoin kucoin-api

0.5 match 39 stars 6.66 score 26 scripts

schweflo

xmlrpc2:Implementation of the Remote Procedure Call Protocol ('XML-RPC')

The 'XML-RPC' is a remote procedure call protocol based on 'XML'. The 'xmlrpc2' package is inspired by the 'XMLRPC' package but uses the 'curl' and 'xml2' packages instead 'RCurl' and 'XML'.

Maintained by Florian Schwendinger. Last updated 7 years ago.

0.5 match 1.48 score 5 scripts 1 dependents