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microseq (version 2.1.6)
Basic Biological Sequence Handling
Description
Basic functions for microbial sequence data analysis. The idea is to use generic R data structures as much as possible, making R data wrangling possible also for sequence data.
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2.1.6
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Install
install.packages('microseq')
Monthly Downloads
696
Version
2.1.6
License
GPL-2
Maintainer
Lars Snipen
Last Published
August 21st, 2023
Functions in microseq (2.1.6)
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Replace amino acids with codons
readGFF
Reading and writing GFF-tables
muscle
Multiple alignment using MUSCLE
orfSignature
Signature for each ORF
msaTrim
Trimming multiple sequence alignments
orfLength
Length of ORF
msalign
Multiple alignment
reverseComplement
Reverse-complementation of DNA
readFastq
Read and write FASTQ files
translate
Translation according to the standard genetic code
readFasta
Read and write FASTA files
microseq-package
Basic Biological Sequence Analysis
iupac2regex
Ambiguity symbol conversion
gregexpr
Extended
gregexpr
with substring retrieval
findrRNA
Finding rRNA genes
gff2fasta
Retrieving annotated sequences
lorfs
Longest ORF
findGenes
Finding coding genes
findOrfs
Finding ORFs in genomes
msa2mat
Convert alignment to matrix