Basic Sequence Processing Tool for Biological Data
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Documentation for package ‘baseq’ version 0.2.0
Help Pages
| as_baseq_dna | S3 DNA Class |
| as_baseq_rna | S3 RNA Class |
| as_Biostrings | Bioconductor Bridge |
| calculate_assembly_stats | Assembly Stats |
| calculate_charge | Protein Net Charge |
| calculate_codon_usage | Codon Usage RSCU |
| calculate_identity | Sequence Identity |
| calculate_mw | Protein MW |
| calculate_pi | Protein pI |
| calculate_tm | Primer Tm |
| clean_file | Batch File Cleaner |
| clean_seq | Universal Sequence Cleaner |
| count_bases | Count Bases |
| count_kmers | K-mer Counting |
| count_pattern | Count Pattern |
| dna_to_protein | Translate DNA to Protein |
| dna_to_rna | DNA to RNA |
| fastq_to_fasta | Convert FASTQ to FASTA |
| filter_fastq_quality | Quality Filter FASTQ |
| find_cpg_islands | CpG Island Detection |
| find_longest_orf | Find Longest ORF |
| gc_content | GC Content |
| get_genetic_code | Get Genetic Code |
| plot_aa_composition | Plot AA Composition |
| plot_dotplot | Plot Dot Plot |
| plot_gc_skew | Plot GC Skew |
| plot_hydrophobicity | Plot Hydrophobicity |
| read_seq | Universal Sequence Reader |
| reverse_translate | Reverse Translation |
| rev_comp | Universal Reverse Complement |
| rna_to_dna | RNA to DNA |
| rna_to_protein | Translate RNA to Protein |
| sars_fragment | SARS-CoV-2 Genome Fragment |
| search_motif | Motif Searching |
| shuffle_sequence | Shuffle Sequence |
| simulate_digestion | Virtual Digestion |
| simulate_fasta | Simulate FASTA File |
| simulate_fastq | Simulate FASTQ File |
| simulate_pcr | PCR Simulator |
| simulate_sequence | Simulate Sequence |
| summarize_fasta | FASTA Summary |
| translate | Generic Translate |
| write_seq | Universal Sequence Writer |