microseq: Basic Biological Sequence Analysis

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Basic functions for microbial sequence data analysis. In some cases the functions use the corresponding functions in the 'Biostrings' package from Bioconductor <http://www.bioconductor.org/>, but provide an easier interface.

Author
Lars Snipen, Kristian Hovde Liland
Date of publication
2016-07-27 03:49:42
Maintainer
Lars Snipen <lars.snipen@nmbu.no>
License
GPL-2
Version
1.0

View on CRAN

Man pages

amplicon
Primer matching
cmalign
Multiple alignment using Infernal
gregexpr
Extended 'gregexpr' with substring retrieval
microseq-package
Basic Biological Sequence Analysis
msalign
Multiple alignment
msaTrim
Trimming multiple sequence alignments
muscle
Multiple alignment using MUSCLE
plot.Fasta
Plotting and summary of 'Fasta' objects
readFasta-and-writeFasta
Read and write FASTA files
readFastq
Read FASTQ files
reverseComplement
Reverse-complementation of DNA
translate
Translation according to the standard genetic code

Files in this package

microseq
microseq/inst
microseq/inst/extdata
microseq/inst/extdata/16S.fasta
microseq/inst/extdata/small.fasta
microseq/inst/extdata/ssu_bacteria.cm
microseq/inst/extdata/small.fastq
microseq/inst/extdata/msa.fasta
microseq/NAMESPACE
microseq/R
microseq/R/microseq-package.R
microseq/R/primers.R
microseq/R/utilityfun.R
microseq/R/multialign.R
microseq/R/dnaManipulate.R
microseq/R/fastq.R
microseq/R/fasta.R
microseq/MD5
microseq/DESCRIPTION
microseq/man
microseq/man/amplicon.Rd
microseq/man/gregexpr.Rd
microseq/man/readFastq.Rd
microseq/man/readFasta-and-writeFasta.Rd
microseq/man/plot.Fasta.Rd
microseq/man/translate.Rd
microseq/man/cmalign.Rd
microseq/man/muscle.Rd
microseq/man/msalign.Rd
microseq/man/microseq-package.Rd
microseq/man/reverseComplement.Rd
microseq/man/msaTrim.Rd