{ "_id": "6a1571cbacfb0bcc41d65339", "Package": "debar", "Type": "Package", "Title": "A Post-Clustering Denoiser for COI-5P Barcode Data", "Version": "1.0.1", "Author": "Cameron M. Nugent", "Maintainer": "Cameron M. Nugent ", "Description": "The 'debar' sequence processing pipeline is designed for\ndenoising high throughput sequencing data for the animal DNA\nbarcode marker cytochrome c oxidase I (COI). The package is\ndesigned to detect and correct insertion and deletion errors\nwithin sequencer outputs. This is accomplished through\ncomparison of input sequences against a profile hidden Markov\nmodel (PHMM) using the Viterbi algorithm (for algorithm details\nsee Durbin et al. 1998, ISBN: 9780521629713). Inserted base\npairs are removed and deleted base pairs are accounted for\nthrough the introduction of a placeholder character. Since the\nPHMM is a probabilistic representation of the COI barcode,\ncorrections are not always perfect. For this reason 'debar'\ncensors base pairs adjacent to reported indel sites, turning\nthem into placeholder characters (default is 7 base pairs in\neither direction, this feature can be disabled). Testing has\nshown that this censorship results in the correct sequence\nlength being restored, and erroneous base pairs being masked\nthe vast majority of the time (>95%).", "License": "GPL-3", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.1", "Config/pak/sysreqs": "make libjpeg-dev libssl-dev zlib1g-dev", "Repository": "https://cnuge.r-universe.dev", "Date/Publication": "2024-01-12 11:23:48 UTC", "RemoteUrl": "https://github.com/cnuge/debar", "RemoteRef": "HEAD", "RemoteSha": "bbd56431ad1b362ec255be6ff704fbd99c4a78fa", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 10:07:37 UTC", "User": "root" }, "MD5sum": "e1edfb6c419157953ca3d9942ab90844", "_user": "cnuge", "_type": "src", "_file": "debar_1.0.1.tar.gz", "_fileid": "185ec8d14730a7f045d604f697c51ab9ba8f4254e6066c4f4318e5ee13859898", "_filesize": 431758, "_sha256": "185ec8d14730a7f045d604f697c51ab9ba8f4254e6066c4f4318e5ee13859898", "_created": "2026-05-26T10:07:37.000Z", "_published": "2026-05-26T10:11:23.806Z", "_distro": "noble", "_jobs": [ { "job": 77852229340, "time": 174, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7214369168" }, { "job": 77852229469, "time": 164, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7214365933" }, { "job": 77852229285, "time": 196, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7214364325" }, { "job": 77852229321, "time": 182, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7214364574" }, { "job": 77851732891, "time": 186, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7214311883" }, { "job": 77852229290, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7214348693" }, { "job": 77852229296, "time": 134, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7214355992" }, { "job": 77852229446, "time": 131, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7214355266" }, { "job": 77852229303, "time": 120, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7214351939" } ], "_buildurl": "https://github.com/r-universe/cnuge/actions/runs/26445792417", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/cnuge/debar", "_commit": { "id": "bbd56431ad1b362ec255be6ff704fbd99c4a78fa", "author": "CNuge ", "committer": "CNuge ", "message": "updating README and docstrings\n", "time": 1705058628 }, "_maintainer": { "name": "Cameron M. Nugent", "email": "camnugent@gmail.com", "login": "cnuge", "description": "Lead Bioinformatician | Sequence Bio", "uuid": 17327173 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "ape", "role": "Imports" }, { "package": "aphid", "role": "Imports" }, { "package": "seqinr", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "coil", "role": "Suggests" } ], "_owner": "cnuge", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "bioinformatics", "denoising", "dna-barcoding", "dna-sequencing", "hidden-markov-model", "machine-learning" ], "_stars": 1, "_contributors": [ { "user": "cnuge", "count": 171, "uuid": 17327173 } ], "_userbio": { "uuid": 17327173, "type": "user", "name": "Cam Nugent", "description": "Lead Bioinformatician | Sequence Bio" }, "_downloads": { "count": 162, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/debar" }, "_devurl": "https://github.com/cnuge/debar", "_searchresults": 8, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/debar.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/cnuge/debar", "_realowner": "cnuge", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2019-12-22" }, { "version": "0.1.1", "date": "2024-01-12" } ], "_exports": [ "aa_check", "aa_check.DNAseq", "adj_seq", "adjust", "adjust.DNAseq", "censored_translation", "col_mode", "consensus_sequence", "denoise", "denoise_file", "denoise_file.default", "denoise_list", "denoise.default", "dir_check", "DNAseq", "ex_nt_list", "example_nt_string", "example_nt_string_errors", "frame", "frame.DNAseq", "individual_DNAbin", "ins_front_trim", "leading_ins", "meta_check", "new_DNAseq", "nt_coi_PHMM", "outseq", "outseq.DNAseq", "print.DNAseq", "read_fasta", "read_fastq", "rev_comp", "set_frame", "translate_codon", "triple_dels", "triple_ins", "validate_DNAseq", "write_fasta", "write_fasta.DNAseq", "write_fastq", "write_fastq.DNAseq", "write_wrapper", "write_wrapper.DNAseq" ], "_help": [ { "page": "aa_check", "title": "Translate a sequence and assess it for the presence of stop codons.", "topics": [ "aa_check", "aa_check.DNAseq" ] }, { "page": "adjust", "title": "Adjust the sequences based on the nt path outputs.", "topics": [ "adjust", "adjust.DNAseq" ] }, { "page": "censored_translation", "title": "Censored Translation of a DNA string.", "topics": [ "censored_translation" ] }, { "page": "consensus", "title": "Take the list of denoised sequences and obtain the consensus sequence.", "topics": [ "consensus", "consensus_sequence" ] }, { "page": "debar", "title": "'debar'", "topics": [ "debar" ] }, { "page": "denoise", "title": "Run the denoiser pipeline for a sequence read.", "topics": [ "denoise", "denoise.default" ] }, { "page": "denoise_file", "title": "Denoise sequence data from a given file.", "topics": [ "denoise_file", "denoise_file.default" ] }, { "page": "denoise_list", "title": "List-to-list denoising of COI barcode sequences.", "topics": [ "denoise_list" ] }, { "page": "dir_check", "title": "Take an input sequence and align both the forward and reverse compliments to the PHMM.", "topics": [ "dir_check" ] }, { "page": "DNAseq", "title": "Build a DNAseq object from a DNA sequence string.", "topics": [ "DNAseq" ] }, { "page": "ex_nt_list", "title": "An example of a list of four coi5p sequences, each containing indel errors.", "topics": [ "ex_nt_list" ] }, { "page": "example_nt_string", "title": "Example coi5p DNA sequence string.", "topics": [ "example_nt_string" ] }, { "page": "example_nt_string_errors", "title": "Example coi5p DNA sequence string with insertion and deletion errors.", "topics": [ "example_nt_string_errors" ] }, { "page": "frame", "title": "Take a DNAseq object and isolate the COI-5P region.", "topics": [ "frame", "frame.DNAseq" ] }, { "page": "outseq", "title": "Get the final denoised output sequence for a read.", "topics": [ "outseq", "outseq.DNAseq" ] }, { "page": "read_fasta", "title": "Read in raw data from a fasta file.", "topics": [ "read_fasta" ] }, { "page": "read_fastq", "title": "Read in raw data from a fastq file.", "topics": [ "read_fastq" ] }, { "page": "write_fasta", "title": "Output the denoised consensus sequence to a fasta file.", "topics": [ "write_fasta", "write_fasta.DNAseq" ] }, { "page": "write_fastq", "title": "Output the denoised sequence to a fastq format with placeholder phred scores.", "topics": [ "write_fastq", "write_fastq.DNAseq" ] } ], "_readme": "https://github.com/cnuge/debar/raw/HEAD/README.md", "_rundeps": [ "ade4", "ape", "aphid", "askpass", "curl", "digest", "kmer", "lattice", "MASS", "nlme", "openssl", "phylogram", 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