baseq
Basic Sequence Processing Tool for Biological Data
Primarily created as an easy and understanding way to do basic sequences surrounding the central dogma of molecular biology.
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.
🚀 Quick Reference (Cheat Sheet)
| Task | Function | Description |
|---|---|---|
| I/O | read_seq() |
Reads FASTA/FASTQ into DataFrames or Lists. |
write_seq() |
Writes DataFrames/Lists to FASTA/FASTQ. | |
| Cleaning | clean_seq() |
Auto-detects DNA/RNA and removes non-bases. |
filter_fastq_quality() |
Filters large FASTQ files by Phred score. | |
| Central Dogma | dna_to_protein() |
6-frame translation (optimized). |
rev_comp() |
Universal reverse complement (DNA/RNA). | |
dna_to_rna() |
Transcription (T -> U). | |
| Discovery | find_longest_orf() |
Scans all frames for the longest gene. |
search_motif() |
Finds regex motifs with coordinates. | |
summarize_fasta() |
Returns a "Genomic Report Card" for a file. | |
| Lab Math | calculate_tm() |
PCR Primer melting temperature. |
calculate_mw() |
Protein molecular weight (Daltons). | |
simulate_pcr() |
Predicts PCR amplicon size from primers. | |
| Plots | plot_gc_skew() |
Visualizes G-C distribution. |
plot_dotplot() |
Visual comparison of two sequences. |
New in Version 0.2.0
- Performance: Core functions are now vectorized and significantly faster.
- Unified API: Smart wrappers like
read_seqandclean_seqauto-detect your data. - Discovery: Added ORF finding, Assembly stats, and wet-lab simulators.
- Visuals: New publication-quality plots using
ggplot2.
Installation
# Install from CRAN (v0.1.4)
install.packages("baseq")
# Install the latest dev version (v0.2.0)
# devtools::install_github("ambuvjyn/baseq")
Getting Started
See the package vignette:
vignette("baseq-vignette", package = "baseq")