Package: coil 1.2.4
coil: Contextualization and Evaluation of COI-5P Barcode Data
Designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI). It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing the likelihood that a given barcode sequence includes an insertion or deletion error. The error assessment relies on the comparison of input sequences against nucleotide and amino acid profile hidden Markov models (PHMMs) (for details see Durbin et al. 1998, ISBN: 9780521629713) trained on a taxonomically diverse set of reference sequences. The functions are provided as a complete pipeline and are also available individually for efficient and targeted analysis of barcode data.
Authors:
coil_1.2.4.tar.gz
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coil.pdf |coil.html✨
coil/json (API)
| # Install 'coil' in R: |
| install.packages('coil', repos = c('https://cnuge.r-universe.dev', 'https://cloud.r-project.org')) |
- example_barcode_data - Example barcode data.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 8 months agofrom:6ef5803d36. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 09 2024 |
| R-4.5-win | NOTE | Sep 09 2024 |
| R-4.5-linux | NOTE | Sep 09 2024 |
| R-4.4-win | OK | Sep 09 2024 |
| R-4.4-mac | OK | Sep 09 2024 |
| R-4.3-win | OK | Sep 09 2024 |
| R-4.3-mac | OK | Sep 09 2024 |
Exports:aa_coi_PHMMcensored_translationcoi5pcoi5p_pipeexample_barcode_dataexample_nt_stringflatten_coi5pframeframe.coi5pindel_checkindel_check.coi5pindividual_AAbinindividual_DNAbinins_front_trimleading_insnew_coi5pnt_coi_PHMMprint.coi5pset_framesubsetPHMMtrans_dftranslatetranslate_codontranslate.coi5pvalidate_coi5pwhich_trans_table
Dependencies:ade4apeaphidaskpassdigestkmerlatticeMASSnlmeopensslphylogrampixmapRcppRcppArmadillosegmentedseqinrspsys
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Amino acid profile hidden Markov model for coi5p. | aa_coi_PHMM |
| Censored Translation of a DNA string. | censored_translation |
| Build a coi5p object from a DNA sequence string. | coi5p |
| Run the entire coi5p pipeline for an input sequence. | coi5p_pipe |
| 'coil': evaluation of COI-5P barcode data | coil |
| Example barcode data. | example_barcode_data |
| Example coi5p DNA sequence string | example_nt_string |
| Flatten a list of coi5p output objects into a dataframe. | flatten_coi5p |
| Take a coi5p sequence and place it in reading frame. | frame frame.coi5p |
| Check if a coi5p sequence likely contains an error. | indel_check indel_check.coi5p |
| Nucleotide profile hidden Markov model for coi5p. | nt_coi_PHMM |
| Subset an existing PHMM. | subsetPHMM |
| Data frame containing the translation table recommendation. | trans_df |
| Translate a coi5p sequence. | translate translate.coi5p |
| Determine the translation table to use for a given taxonomic group. | which_trans_table |
