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microseq (version 1.3)

Basic Biological Sequence Handling

Description

Basic functions for microbial sequence data analysis. The idea is to use the basic R data structures as much as possible, without building complex data types.

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Version

Install

install.packages('microseq')

Monthly Downloads

587

Version

1.3

License

GPL-2

Maintainer

Lars Snipen

Last Published

October 27th, 2019

Functions in microseq (1.3)

msaTrim

Trimming multiple sequence alignments
findOrfs

Finding ORFs in genomes
gregexpr

Extended gregexpr with substring retrieval
plot.Fasta

Plotting and summary of Fasta objects
orfLength

ORF lengths
findGenes

Finding coding genes
muscle

Multiple alignment using MUSCLE
lorfs

Longest ORF
reverseComplement

Reverse-complementation of DNA
msalign

Multiple alignment
translate

Translation according to the standard genetic code
iupac2regex

Ambiguity symbol conversion
microseq-package

Basic Biological Sequence Analysis
plot.Fastq

Plotting and summary of Fastq objects
readFasta

Read and write FASTA files
gffSignature

GFF signature text
findrRNA

Finding rRNA genes
readFastq

Read and write FASTQ files
gff2fasta

Retrieving annotated sequences
readGFF

Reading and writing GFF-tables