R: Basic Sequence Processing Tool for Biological Data

# Basic Sequence Processing Tool for Biological Data

## Documentation for package ‘baseq’ version 0.1.4

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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