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baseq (v0.2.0)

Basic Sequence Processing Tool for Biological Data

Developed by Ambu Vijayan and Dr. J. Sreekumar

baseq is a comprehensive "Molecular Biology Starter Kit" for R. It provides simple, efficient, and well-tested functions for common tasks in sequence processing, analysis, and visualization.

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Install

install.packages('baseq')

Monthly Downloads

251

Version

0.2.0

License

GPL-3

Issues

0

Pull Requests

0

Stars

4

Forks

0

Maintainer

Ambu Vijayan

Last Published

March 12th, 2026

Functions in baseq (0.2.0)

sars_fragment

SARS-CoV-2 Genome Fragment
gc_content

GC Content
plot_gc_skew

Plot GC Skew
rna_to_protein

Translate RNA to Protein
rna_to_dna

RNA to DNA
clean_seq

Universal Sequence Cleaner
plot_dotplot

Plot Dot Plot
simulate_sequence

Simulate Sequence
get_genetic_code

Get Genetic Code
simulate_pcr

PCR Simulator
plot_aa_composition

Plot AA Composition
fastq_to_fasta

Convert FASTQ to FASTA
dna_to_rna

DNA to RNA
shuffle_sequence

Shuffle Sequence
search_motif

Motif Searching
find_cpg_islands

CpG Island Detection
translate

Generic Translate
simulate_fastq

Simulate FASTQ File
rev_comp

Universal Reverse Complement
summarize_fasta

FASTA Summary
reverse_translate

Reverse Translation
simulate_fasta

Simulate FASTA File
simulate_digestion

Virtual Digestion
write_seq

Universal Sequence Writer
calculate_tm

Primer Tm
calculate_pi

Protein pI
calculate_codon_usage

Codon Usage RSCU
as_Biostrings

Bioconductor Bridge
calculate_charge

Protein Net Charge
as_baseq_rna

S3 RNA Class
calculate_mw

Protein MW
find_longest_orf

Find Longest ORF
calculate_identity

Sequence Identity
calculate_assembly_stats

Assembly Stats
as_baseq_dna

S3 DNA Class
filter_fastq_quality

Quality Filter FASTQ
plot_hydrophobicity

Plot Hydrophobicity
count_bases

Count Bases
count_kmers

K-mer Counting
count_pattern

Count Pattern
clean_file

Batch File Cleaner
dna_to_protein

Translate DNA to Protein
read_seq

Universal Sequence Reader