stitam
. See also theR-universe documentation.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:
webseq_0.1.tar.gz
webseq_0.1.zip(r-4.5)webseq_0.1.zip(r-4.4)webseq_0.1.zip(r-4.3)
webseq_0.1.tgz(r-4.4-any)webseq_0.1.tgz(r-4.3-any)
webseq_0.1.tar.gz(r-4.5-noble)webseq_0.1.tar.gz(r-4.4-noble)
webseq_0.1.tgz(r-4.4-emscripten)webseq_0.1.tgz(r-4.3-emscripten)
webseq.pdf |webseq.html✨
webseq/json (API)
# Install 'webseq' in R: |
install.packages('webseq', repos = c('https://staging.r-multiverse.org', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stitam/webseq/issues
- examples - Examples
Last updated 11 months agofrom:b710f93da5 (on b710f93da5b8dd8a30fa170cdf3da8da943fbae1). Checks:OK: 1 WARNING: 6. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 13 2024 |
R-4.5-win | WARNING | Nov 13 2024 |
R-4.5-linux | WARNING | Nov 13 2024 |
R-4.4-win | WARNING | Nov 13 2024 |
R-4.4-mac | WARNING | Nov 13 2024 |
R-4.3-win | WARNING | Nov 13 2024 |
R-4.3-mac | WARNING | Nov 13 2024 |
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:askpassclicpp11curldplyrfansigenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigplyrpurrrR6Rcpprentrezrlangstringistringrsystibbletidyrtidyselectutf8vctrswithrXMLxml2
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 |