Package: baseq 0.1.1

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.

Authors:Ambu Vijayan [aut, cre], J. Sreekumar [aut]

# Install 'baseq' in R:

install.packages('baseq', repos = c('https://ambuvjyn.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Last updated 1 years agofrom:44f6d75d23. Checks:OK: 1 NOTE: 6. Indexed: yes.

Dependencies:

Last update: 2023-04-26
Started: 2023-04-26

Help page	Topics
Clean DNA file	clean_DNA_file
Clean DNA sequence	clean_DNA_sequence
Clean RNA file	clean_RNA_file
Clean RNA sequence	clean_RNA_sequence
Clean DNA or RNA sequence	clean_sequence
Count the number of A's, C's, G's, and T's in a DNA sequence	count_bases
Count frequency of a pattern in a sequence	count_seq_pattern
Translation of a DNA sequence	dna_to_protein
Transcription of a DNA sequence	dna_to_rna
Convert a FASTQ file to a FASTA file	fastq_to_fasta
Calculate GC content of a DNA sequence	gc_content
GC content of sequences in a multi FASTA file	gc_content_file
Read a fasta file into a dataframe and assign to the environment	read.fasta_to_df
Read a fasta file into a list and assign to the environment	read.fasta_to_list
Read a Fastq file and store it as a dataframe	read.fastq_to_df
Read a Fastq file and store it as a list	read.fastq_to_list
Generate Reverse Complement of DNA sequence	reverse_complement
Generate Reverse Complement of DNA sequence	rna_reverse_complement
Reverse Transcription of a RNA sequence	rna_to_dna
Translation of a RNA sequence	rna_to_protein
Write a data frame to a fasta file	write.df_to_fasta
Write a FASTQ file from a dataframe of reads	write.df_to_fastq
Write a list of sequences to a FASTA file	write.list_to_fasta
Write a list of sequences and quality scores to a FASTQ file	write.list_to_fastq