R-universe search: topic: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

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 5 days ago.

curl

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

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 4 days ago.

infrastructure dataimport hdf5 rhdf5 openssl curl zlib cpp

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

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

459 stars 14.63 score 948 scripts 18 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

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 3 days ago.

annotation visualization dataimport zlib openssl curl

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 28 days ago.

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

220 stars 11.80 score 578 scripts 3 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

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 23 days ago.

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

11 stars 11.25 score 3 scripts 591 dependents

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 24 days ago.

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

77 stars 10.06 score 165 scripts

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 3 months ago.

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

68 stars 9.02 score 84 scripts

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

47 stars 8.98 score 66 scripts 7 dependents

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

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

6 stars 8.63 score 79 scripts 1 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 6 days ago.

curl

2 stars 8.50 score 1.0k 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

8.32 score 498 scripts 7 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

49 stars 8.29 score 141 scripts 1 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 12 months ago.

curl zlib cpp

67 stars 8.23 score 49 scripts 11 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

148 stars 8.12 score 111 scripts 5 dependents

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

15 stars 8.07 score 36 scripts 24 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 18 days ago.

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

31 stars 7.95 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

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

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 14 days ago.

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

13 stars 6.70 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

6.53 score 38 scripts 1 dependents

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

36 stars 6.16 score 812 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

8 stars 5.98 score 6 scripts

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 23 days ago.

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

4 stars 5.94 score 5 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 3 months ago.

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

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

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

5.02 score 6 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

1 stars 4.48 score 9 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

4.48 score 2 scripts

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

5 stars 3.40 score 10 scripts

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

2.60 score

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

3 stars 2.18 score