Package: microseq 2.1.6

microseq: Basic Biological Sequence Handling

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.

Authors:Lars Snipen, Kristian Hovde Liland

microseq_2.1.6.tar.gz
microseq_2.1.6.zip(r-4.5)microseq_2.1.6.zip(r-4.4)microseq_2.1.6.zip(r-4.3)
microseq_2.1.6.tgz(r-4.4-x86_64)microseq_2.1.6.tgz(r-4.4-arm64)microseq_2.1.6.tgz(r-4.3-x86_64)microseq_2.1.6.tgz(r-4.3-arm64)
microseq_2.1.6.tar.gz(r-4.5-noble)microseq_2.1.6.tar.gz(r-4.4-noble)
microseq_2.1.6.tgz(r-4.4-emscripten)microseq_2.1.6.tgz(r-4.3-emscripten)
microseq.pdf |microseq.html✨
microseq/json (API)

# Install 'microseq' in R:

install.packages('microseq', repos = c('https://larssnip.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/larssnip/microseq/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

5.45 score 3 stars 3 packages 52 scripts 603 downloads 23 exports 20 dependencies

Last updated 6 months agofrom:1bf4da28cd. Checks:OK: 4 NOTE: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win-x86_64	NOTE	Oct 31 2024
R-4.5-linux-x86_64	NOTE	Oct 31 2024
R-4.4-win-x86_64	NOTE	Oct 31 2024
R-4.4-mac-x86_64	NOTE	Oct 31 2024
R-4.4-mac-aarch64	NOTE	Oct 31 2024
R-4.3-win-x86_64	OK	Oct 31 2024
R-4.3-mac-x86_64	OK	Oct 31 2024
R-4.3-mac-aarch64	OK	Oct 31 2024

Exports:backTranslate findGenes findOrfs findrRNA gff2fasta gregexpr iupac2regex lorfs msa2mat msalign msaTrim muscle orfLength orfSignature readFasta readFastq readGFF regex2iupac reverseComplement translate writeFasta writeFastq writeGFF

Dependencies:cli data.table dplyr fansi generics glue lifecycle magrittr pillar pkgconfig R6 Rcpp rlang stringi stringr tibble tidyselect utf8 vctrs withr

The microseq package vignette

Rendered fromvignette.Rnwusingutils::Sweaveon Oct 31 2024.

Last update: 2022-07-05
Started: 2017-08-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Basic Biological Sequence Analysis	microseq-package microseq
Replace amino acids with codons	backTranslate
Finding coding genes	findGenes
Finding ORFs in genomes	findOrfs
Finding rRNA genes	findrRNA
Retrieving annotated sequences	gff2fasta
Extended 'gregexpr' with substring retrieval	gregexpr
Ambiguity symbol conversion	iupac2regex regex2iupac
Longest ORF	lorfs
Convert alignment to matrix	msa2mat
Multiple alignment	msalign
Trimming multiple sequence alignments	msaTrim
Multiple alignment using MUSCLE	muscle
Length of ORF	orfLength
Signature for each ORF	orfSignature
Read and write FASTA files	readFasta writeFasta
Read and write FASTQ files	readFastq writeFastq
Reading and writing GFF-tables	readGFF writeGFF
Reverse-complementation of DNA	reverseComplement
Translation according to the standard genetic code	translate