Basic Sequence Processing Tool for Biological Data

Documentation for package ‘baseq’ version 0.1.4

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