Package: Map2NCBI 1.4
Map2NCBI: Mapping Markers to the Nearest Genomic Feature
Allows the user to generate a list of features (gene, pseudo, RNA, CDS, and/or UTR) directly from NCBI database for any species with a current build available. Option to save downloaded and formatted files is available, and the user can prioritize the feature list based on type and assembly builds present in the current build used. The user can then use the list of features generated or provide a list to map a set of markers (designed for SNP markers with a single base pair position available) to the closest feature based on the map build. This function does require map positions of the markers to be provided and the positions should be based on the build being queried through NCBI.
Authors:
Map2NCBI_1.4.tar.gz
Map2NCBI_1.4.zip(r-4.5)Map2NCBI_1.4.zip(r-4.4)Map2NCBI_1.4.zip(r-4.3)
Map2NCBI_1.4.tgz(r-4.4-any)Map2NCBI_1.4.tgz(r-4.3-any)
Map2NCBI_1.4.tar.gz(r-4.5-noble)Map2NCBI_1.4.tar.gz(r-4.4-noble)
Map2NCBI_1.4.tgz(r-4.4-emscripten)Map2NCBI_1.4.tgz(r-4.3-emscripten)
Map2NCBI.pdf |Map2NCBI.html✨
Map2NCBI/json (API)
| # Install 'Map2NCBI' in R: |
| install.packages('Map2NCBI', repos = c('https://lauren-hanna.r-universe.dev', 'https://cloud.r-project.org')) |
- Example10MarkerFile - Example Marker File with 10 Markers on BTA 1
- GeneList_BTA1 - Output from GetGeneList function for BTA 1
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 years agofrom:8410a79980. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 17 2024 |
| R-4.5-win | NOTE | Nov 17 2024 |
| R-4.5-linux | NOTE | Nov 17 2024 |
| R-4.4-win | OK | Nov 17 2024 |
| R-4.4-mac | OK | Nov 17 2024 |
| R-4.3-win | OK | Nov 17 2024 |
| R-4.3-mac | OK | Nov 17 2024 |
Exports:GetGeneListMapMarkers
Dependencies:askpasscurlhttrjsonlitemimeopensslR6rentrezsysXML
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Mapping Markers to the Nearest Genomic Feature | Map2NCBI-package Map2NCBI |
| Example Marker File with 10 Markers on BTA 1 | Example10MarkerFile |
| Output from GetGeneList function for BTA 1 | GeneList_BTA1 |
| A Function to Filter and Save Genomic Features from NCBI (all builds) | GetGeneList |
| Mapping SNP Markers to Closest Genomic Feature | MapMarkers |
