Introduction | Run the Pipeline | Messages and Warnings | Optional: Write CSV/PDF outputs | Visualize Summary Plots | Alignment length histogram | Assignment summary bar chart | Phylum level stacked bar chart | Review Tabular Outputs | Step Summary Table | Unique Taxa Counts Table | (Optional) Save the multi-page PDF | Display Final Assignments Table | Conclusion
Package: ClassifyITS 1.0.3
ClassifyITS: Fungal Assignment Pipeline
Fungi are ubiquitous in Earth's wonderfully diverse ecosystems. The 'ClassifyITS' package aids in the taxonomic classification of internal transcribed spacer (ITS) fungal sequences. Unlike previous methods, it employs taxon-specific e-value and percent identity cutoffs at each taxonomic rank from kingdom to species. The package takes a conservative approach and outputs both graphics and user-friendly files to help users manually inspect fungal operational taxonomic units (OTUs) that fail classification at relevant levels (e.g., Phylum). 'ClassifyITS' is based on taxonomic cutoff criteria from "The Global Soil Mycobiome consortium dataset for boosting fungal diversity research" (Fungal Diversity, Tedersoo, 2021, <doi:10.1007/s13225-021-00493-7>) and "Best practices in metabarcoding of fungi: From experimental design to results" (Molecular Ecology, Tedersoo, 2022, <doi:10.1111/mec.16460>).
Authors:
ClassifyITS_1.0.3.tar.gz
ClassifyITS_1.0.3.zip(r-4.7-any)ClassifyITS_1.0.3.zip(r-4.6-any)ClassifyITS_1.0.3.zip(r-4.5-any)
ClassifyITS_1.0.3.tgz(r-4.6-any)ClassifyITS_1.0.3.tgz(r-4.5-any)
ClassifyITS_1.0.3.tar.gz(r-4.7-any)ClassifyITS_1.0.3.tar.gz(r-4.6-any)
ClassifyITS_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ClassifyITS/json (API)
| # Install 'ClassifyITS' in R: |
| install.packages('ClassifyITS', repos = c('https://qmoon11.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/qmoon11/classifyits/issues
Last updated from:865a279881. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 126 | ||
| source / vignettes | OK | 187 | ||
| linux-release | OK | 135 | ||
| macos-release | OK | 182 | ||
| macos-oldrel | OK | 157 | ||
| windows-devel | OK | 77 | ||
| windows-release | OK | 70 | ||
| windows-oldrel | OK | 65 | ||
| wasm-release | OK | 100 |
Exports:best_hit_taxonomy_assignmentcheck_Nconsensus_taxonomy_assignmenteasy_assignmentsensure_colsITS_assignmentload_and_checkparse_taxonomy_cutoffsplot_alignment_histsafe_rbind_listsave_taxonomy_graphicstrim_alignmentswrite_initial_assignments
Dependencies:ade4clicpp11data.tablefarverggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSnlmepixmapplyrR6RColorBrewerRcppRcppArmadilloreshape2rlangS7scalessegmentedseqinrspstringistringrvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Hierarchical best-hit taxonomy assignment with per-rank fallback rule | best_hit_taxonomy_assignment |
| Check proportion of N bases in each sequence. | check_N |
| Per-rank consensus filter for taxonomy assignment | consensus_taxonomy_assignment |
| Easy taxonomy assignment for OTUs using BLAST QC output & phylum-specific thresholds. | easy_assignments |
| Ensure data frame has all required columns (as character) | ensure_cols |
| Complete Fungal Assignment Pipeline | ITS_assignment |
| Load and check BLAST results and rep-seq FASTA | load_and_check |
| Parse taxonomy cutoffs file | parse_taxonomy_cutoffs |
| Create and return alignment length histogram (ggplot object) | plot_alignment_hist |
| Safely rbinds list of data frames, ensuring columns match | safe_rbind_list |
| Save taxonomy summary charts and tables to multi-page PDF | save_taxonomy_graphics |
| Trim BLAST alignments by minimum length | trim_alignments |
| Create and write the initial assignments table including drops at all steps | write_initial_assignments |