https://github.com/zachcp/flattax
Flat NCBI Taxonomy Table
https://github.com/zachcp/flattax
Last synced: 3 months ago
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Flat NCBI Taxonomy Table
- Host: GitHub
- URL: https://github.com/zachcp/flattax
- Owner: zachcp
- Created: 2020-07-01T20:19:35.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2020-10-13T19:27:57.000Z (over 4 years ago)
- Last Synced: 2025-02-24T04:13:00.449Z (3 months ago)
- Language: R
- Size: 58.9 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# flattax
The goal of `flattax` is to provide a simplified view on NCBI's
taxonomic hierarchy. It provides the following datasets:
- `flattax`: A data.table of NCBI's `new_taxdump/rankedlineage.dmp` file.
## Installatation
``` r
# install from github.
devtools::install_github("zachcp/flattax")
```
## Example Usage
```
> library(flattax)
> flattax
tax_id tax_name species genus family order class phylum kingdom
1: 1 root
2: 131567 cellular organisms
3: 2157 Archaea
4: 1935183 Asgard group
5: 1936272 Candidatus Heimdallarchaeota
---
2281047: 2413 Transposon Tn7
2281048: 2417 Transposon Tn9
2281049: 2414 Transposon Tn903
2281050: 2415 Transposon Tn916
2281051: 2416 Transposon Tn917
superkingdom
1:
2:
3:
4: Archaea
5: Archaea
---
2281047:
2281048:
2281049:
2281050:
2281051:
```