Download genome assemblies | Download metadata | Parse metadata files
Package: webseq 0.1
Tamas Stirling
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:
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://r-multiverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stitam/webseq/issues
Datasets:
- examples - Examples
Last updated from:b710f93da5 (on v0.1.0). Checks:7 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | WARNING | 210 | ||
| source / vignettes | OK | 203 | ||
| linux-release-x86_64 | WARNING | 208 | ||
| macos-release-arm64 | WARNING | 160 | ||
| macos-oldrel-arm64 | WARNING | 153 | ||
| windows-devel | WARNING | 133 | ||
| windows-release | WARNING | 142 | ||
| windows-oldrel | WARNING | 146 | ||
| wasm-release | OK | 143 |
Exports:ena_queryextract_accnflag_filesmgnify_endpointsmgnify_instancemgnify_listncbi_download_genomencbi_get_metancbi_link_uidncbi_parsencbi_parse_assembly_xmlncbi_parse_biosample_txtparse_gb_headerparse_report
Dependencies:askpassclicpp11curldplyrgenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigplyrpurrrR6Rcpprentrezrlangstringistringrsystibbletidyrtidyselectutf8vctrswithrXMLxml2
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Retrieve sequences from ENA | ena_query |
| Examples | examples |
| Extract Accession Numbers from a parsed assembly report | extract_accn |
| Flag files to keep for analysis | flag_files |
| 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 | ncbi_download_genome |
| Get sequence metadata from NCBI | ncbi_get_meta |
| Get UID-s from NCBI databases | ncbi_get_uid |
| 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 |
| Parse headers from GenBank files | parse_gb_header |
| Parse assembly reports | parse_report |
