zhang-ncbi/dataset_r_test
R Package Client for NCBI Datasets API

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README.md

README.md
In zhang-ncbi/dataset_r_test: R Package Client for NCBI Datasets API

R API client for ncbi.datasets

NCBI service to query and download biological sequence data across all domains of life from NCBI databases.

Overview

This API client was generated by the OpenAPI Generator project. By using the OpenAPI spec from a remote server, you can easily generate an API client.

Installation

Prerequisites

Install the dependencies

install.packages("jsonlite")
install.packages("httr")
install.packages("caTools")

Build the package

git clone https://github.com/GIT_USER_ID/GIT_REPO_ID
cd GIT_REPO_ID
R CMD build .
R CMD check ncbi.datasets_0.1.0.tar.gz
R CMD INSTALL ncbi.datasets_0.1.0.tar.gz

Install the package

install.packages("ncbi.datasets")

To install directly from Github, use devtools:

install.packages("devtools")
library(devtools)
install_github("GIT_USER_ID/GIT_REPO_ID")

Usage

library(ncbi.datasets)

Documentation for API Endpoints

All URIs are relative to https://api.ncbi.nlm.nih.gov/datasets/v1alpha

Class | Method | HTTP request | Description ------------ | ------------- | ------------- | ------------- GeneApi | DownloadGenePackage | GET /gene/id/{gene_ids}/download | Get a gene dataset by gene ID GeneApi | DownloadGenePackagePost | POST /gene/download | Get a gene dataset by POST GeneApi | GeneDownloadSummaryByAccession | GET /gene/accession/{accessions}/download_summary | Get gene download summary by RefSeq Accession GeneApi | GeneDownloadSummaryById | GET /gene/id/{gene_ids}/download_summary | Get gene download summary by GeneID GeneApi | GeneDownloadSummaryByPost | POST /gene/download_summary | Get gene download summary GeneApi | GeneDownloadSummaryByTaxAndSymbol | GET /gene/symbol/{symbols}/taxon/{taxon}/download_summary | Get gene download summary by gene symbol. GeneApi | GeneMetadataByAccession | GET /gene/accession/{accessions} | Get gene metadata by RefSeq Accession GeneApi | GeneMetadataById | GET /gene/id/{gene_ids} | Get gene metadata by GeneID GeneApi | GeneMetadataByPost | POST /gene | Get gene metadata GeneApi | GeneMetadataByTaxAndSymbol | GET /gene/symbol/{symbols}/taxon/{taxon} | Get gene metadata by gene symbol. GeneApi | GeneTaxNameQuery | GET /gene/taxon_suggest/{taxon_query} | Get a list of taxonomy names and IDs found in the gene dataset given a partial taxonomic name. GeneApi | GeneTaxTree | GET /gene/taxon/{taxon}/tree | Retrieve tax tree GenomeApi | AssemblyDescriptorsByAccessions | GET /genome/accession/{accessions} | Get genome metadata by accession GenomeApi | AssemblyDescriptorsByTaxon | GET /genome/taxon/{taxon} | Get genome metadata by taxonomic identifier GenomeApi | CheckAssemblyAvailability | GET /genome/accession/{accessions}/check | Check the validity of genome accessions GenomeApi | CheckAssemblyAvailabilityPost | POST /genome/check | Check the validity of many genome accessions in a single request GenomeApi | DownloadAssemblyPackage | GET /genome/accession/{accessions}/download | Get a genome dataset by accession GenomeApi | DownloadAssemblyPackagePost | POST /genome/download | Get a genome dataset by post GenomeApi | GenomeDownloadSummary | GET /genome/accession/{accessions}/download_summary | Preview genome dataset download GenomeApi | GenomeDownloadSummaryByPost | POST /genome/download_summary | Preview genome dataset download by POST GenomeApi | GenomeTaxNameQuery | GET /genome/taxon_suggest/{taxon_query} | Get a list of taxonomy names and IDs found in the assembly dataset given a partial taxonomic name. GenomeApi | GenomeTaxTree | GET /genome/taxon/{taxon}/tree | Get a taxonomic subtree by taxonomic identifier VirusApi | Sars2ProteinDownload | GET /virus/taxon/sars2/protein/{proteins}/download | Download SARS-CoV-2 protein and CDS datasets by protein name VirusApi | Sars2ProteinSummary | GET /virus/taxon/sars2/protein/{proteins} | Summary of SARS-CoV-2 protein and CDS datasets by protein name VirusApi | Sars2ProteinTable | GET /virus/taxon/sars2/protein/{proteins}/table | Get SARS-CoV-2 protein metadata in a tabular format. VirusApi | VirusGenomeDownload | GET /virus/taxon/{taxon}/genome/download | Download Coronavirus genome datasets by taxon VirusApi | VirusGenomeSummary | GET /virus/taxon/{taxon}/genome | Get summary data for Coronaviridae genomes by taxon VirusApi | VirusGenomeTable | GET /virus/taxon/{taxon}/genome/table | Get viral genomic metadata in a tabular format.

Documentation for Models

Documentation for Authorization

All endpoints do not require authorization.

Author



zhang-ncbi/dataset_r_test documentation built on Jan. 1, 2021, 1:52 p.m.

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