Package: bioseq 0.1.4

bioseq: A Toolbox for Manipulating Biological Sequences

Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences). Implements S3 infrastructure to work with biological sequences as described in Keck (2020) <doi:10.1111/2041-210X.13490>. Provides a collection of functions to perform biological conversion among classes (transcription, translation) and basic operations on sequences (detection, selection and replacement based on positions or patterns). The package also provides functions to import and export sequences from and to other package formats.

Authors:Francois Keck [aut, cre, cph]

bioseq_0.1.4.tar.gz
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bioseq.pdf |bioseq.html✨
bioseq/json (API)
NEWS

# Install 'bioseq' in R:
install.packages('bioseq', repos = c('https://fkeck.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fkeck/bioseq/issues

Datasets:
  • fragilaria - DNA sequences (rbcL) for various Fragilaria

On CRAN:

6.94 score 20 stars 2 packages 72 scripts 387 downloads 61 exports 35 dependencies

Last updated 2 years agofrom:bb49efac88. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winOKOct 29 2024
R-4.5-linuxOKOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 2024
R-4.3-winOKOct 29 2024
R-4.3-macOKOct 29 2024

Exports:aaaliviewas_aaas_AAbinas_dnaas_DNAbinas_rnaas_seqinr_alignmentas_tibble.AAbinas_tibble.bioseq_aaas_tibble.bioseq_dnaas_tibble.bioseq_rnaas_tibble.DNAbindnais_aais_dnais_rnanew_aanew_dnanew_rnapillar_shaft.bioseq_aapillar_shaft.bioseq_dnapillar_shaft.bioseq_rnaread_fastarnaseaviewseq_clusterseq_combineseq_complementseq_consensusseq_count_patternseq_crop_patternseq_crop_positionseq_detect_patternseq_disambiguate_IUPACseq_extract_patternseq_extract_positionseq_ncharseq_nseqseq_remove_patternseq_remove_positionseq_replace_patternseq_replace_positionseq_rev_transcribeseq_rev_translateseq_reverseseq_spelloutseq_split_kmerseq_split_patternseq_stat_gcseq_stat_propseq_transcribeseq_translatevalidate_seqvec_cast.bioseq_aavec_cast.bioseq_dnavec_cast.bioseq_rnavec_ptype2.bioseq_aavec_ptype2.bioseq_dnavec_ptype2.bioseq_rnawrite_fasta

Dependencies:apebitbit64clicliprcpp11crayondigestdplyrfansigenericsgluehmslatticelifecyclemagrittrnlmepillarpkgconfigprettyunitsprogressR6Rcppreadrrlangstringdiststringistringrtibbletidyselecttzdbutf8vctrsvroomwithr

Cleaning and exploring NCBI data with the bioseq package

Rendered fromref_database.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2022-08-11
Started: 2020-05-11

Introduction to the bioseq package

Rendered fromintro-bioseq.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2020-05-11
Started: 2020-05-11

Readme and manuals

Help Manual

Help pageTopics
Build an amino acid (AA) vectoraa
AliView: DNA sequences vieweraliview
Biological alphabetsalphabets
Coercion to an amino acid (AA) vectoras_aa
Coerce to AAbinas_AAbin
Coerce tibble to AAbinas_AAbin.tbl_df
Coercion to DNA vectoras_dna
Coerce to DNAbinas_DNAbin
Coerce tibble to DNAbinas_DNAbin.tbl_df
Coercion to RNA vectoras_rna
Coerce to seqinr alignmentas_seqinr_alignment
Convert DNAbin/AAbin to tibbleas-tibble-ape as_tibble.AAbin as_tibble.DNAbin
Convert bioseq DNA, RNA and AA to tibbleas-tibble-bioseq as_tibble.bioseq_aa as_tibble.bioseq_dna as_tibble.bioseq_rna
Genetic code tablesdic_genetic_codes
Build a DNA vectordna
DNA sequences (rbcL) for various Fragilariafragilaria
Genetic code tablesgenetic-codes
Test if the object is an amino acid vectoris_aa
Test if the object is a DNA vectoris_dna
Test if the object is a RNA vectoris_rna
Amino acid (AA) vector constructornew_aa
DNA vector constructornew_dna
RNA vector constructornew_rna
Read sequences in FASTA formatread_fasta
Reverse and complement sequencesrev_complement seq_complement seq_reverse
Build a RNA vectorrna
SeaView: DNA sequences and phylogenetic tree viewerseaview
Cluster sequences by similarityseq_cluster
Combine multiple sequencesseq_combine
Find a consensus sequence for a set of sequences.seq_consensus
Count the number of matches in sequencesseq_count_pattern
Crop sequences using delimiting patternsseq_crop_pattern
Crop sequences between two positionsseq_crop_position
Detect the presence of patterns in sequencesseq_detect_pattern
Disambiguate biological sequencesseq_disambiguate_IUPAC
Extract matching patterns from sequencesseq_extract_pattern
Extract a region between two positions in sequencesseq_extract_position
Count the number of character in sequencesseq_nchar
Number of sequences in a vectorseq_nseq
Remove matched patterns in sequencesseq_remove_pattern
Remove a region between two positions in sequences.seq_remove_position
Replace a region between two positions in sequencesseq_replace_position
Reverse translate amino acid sequencesseq_rev_translate
Spell out sequencesseq_spellout
Split sequences into k-mersseq_split_kmer
Split sequencesseq_split_pattern
Compute G+C contentseq_stat_gc
Compute proportions for charactersseq_stat_prop
Translate DNA/RNA sequences into amino acidsseq_translate
Replace matched patterns in sequencesseq-replace seq_replace_pattern
Transcribe DNA, reverse-transcribe RNAseq_rev_transcribe seq_transcribe transcription
Write sequences in FASTA formatwrite_fasta