Package: webseq 0.1

webseq: Access data from biological sequence databases like NCBI, ENA, MGnify

This package interacts with online biological sequence databases. It provides functions to search for sequences, convert identifiers and download sequences and associated metadata.

Authors:Tamas Stirling

webseq_0.1.tar.gz
webseq_0.1.zip(r-4.7)webseq_0.1.zip(r-4.6)webseq_0.1.zip(r-4.5)
webseq_0.1.tgz(r-4.6-any)webseq_0.1.tgz(r-4.5-any)
webseq_0.1.tar.gz(r-4.7-any)webseq_0.1.tar.gz(r-4.6-any)
webseq_0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
webseq/json (API)

# Install 'webseq' in R:

install.packages('webseq', repos = c('https://stitam.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stitam/webseq/issues

Datasets:

examples - Examples

On CRAN:

3.65 score 3 stars 1 scripts 24 exports 48 dependencies

Last updated from:4337b497f8. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	226
source / vignettes	OK	236
linux-release-x86_64	ERROR	221
macos-release-arm64	ERROR	190
macos-oldrel-arm64	ERROR	199
windows-devel	ERROR	216
windows-release	ERROR	205
windows-oldrel	ERROR	196
wasm-release	OK	120

Exports:dv_connect dv_download dv_list_files ena_download_reads ena_query ena2ncbi extract_accn flag_files mgnify_endpoints mgnify_instance mgnify_list ncbi_download_genome ncbi_get_meta ncbi_get_summary ncbi_get_uid ncbi_link ncbi_link_uid ncbi_parse ncbi_parse_assembly_xml ncbi_parse_biosample_txt ncbi_post_uid ncbi_recover_id ncbi2ena parse_report

Dependencies:askpass backports bit bit64 cachem checkmate cli clipr cpp11 crayon curl dataverse dplyr fastmap generics glue hms httr httr2 jsonlite lifecycle magrittr memoise mime openssl pillar pkgconfig prettyunits progress purrr R6 rappdirs readr rentrez rlang stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr XML xml2

NCBI

Download genome assemblies | Download metadata | Parse metadata files

Rendered fromncbi.Rmdusingknitr::rmarkdown

Last update: 2023-12-10
Started: 2023-08-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Connect to a Dataset on a Dataverse server	dv_connect
Download files from a Dataset on a Dataverse server	dv_download
List files in a Dataset on a Dataverse server	dv_list_files
Download sequencing reads from the European Nucleotide Archive (ENA)	ena_download_reads
Retrieve sequences from ENA	ena_query
Convert accessions from ENA to NCBI	ena2ncbi
Examples	examples
Extract Accession Numbers from a parsed assembly report	extract_accn
Flag files to keep for analysis	flag_files
Bind rows in a list of list of data frames	flatten
MGnify endpoints	mgnify_endpoints
Search for a specific entry in MGnify	mgnify_instance
Retrieve a list of instances from MGnify	mgnify_list
Download Genomes from NCBI Assembly Database	ncbi_download_genome
Get sequence metadata from NCBI	ncbi_get_meta
Get object summary from NCBI	ncbi_get_summary
Get UID-s from NCBI databases	ncbi_get_uid
Link ID-s from one NCBI database to another	ncbi_link
Link UID-s from one NCBI database to another	ncbi_link_uid
Retrieve NCBI Assembly metadata	ncbi_meta_assembly
Parse NCBI sequence metadata	ncbi_parse
Parse NCBI assembly metadata	ncbi_parse_assembly_xml
Parse NCBI BioSample metadata	ncbi_parse_biosample_txt
Parse NCBI BioSample metadata	ncbi_parse_biosample_xml
Post a vector of NCBI UIDs	ncbi_post_uid
Recover NCBI IDs from NCBI UIDs	ncbi_recover_id
Convert accessions from NCBI to ENA	ncbi2ena
Parse assembly reports	parse_report