Package: microseq 2.2.0

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 [aut, cre], Kristian Hovde Liland [aut]

microseq_2.2.0.tar.gz
microseq_2.2.0.zip(r-4.7-x86_64)microseq_2.2.0.zip(r-4.7-arm64)microseq_2.2.0.zip(r-4.6-x86_64)microseq_2.2.0.zip(r-4.6-arm64)microseq_2.2.0.zip(r-4.5-x86_64)
microseq_2.2.0.tgz(r-4.6-x86_64)microseq_2.2.0.tgz(r-4.6-arm64)microseq_2.2.0.tgz(r-4.5-x86_64)microseq_2.2.0.tgz(r-4.5-arm64)
microseq_2.2.0.tar.gz(r-4.7-arm64)microseq_2.2.0.tar.gz(r-4.7-x86_64)microseq_2.2.0.tar.gz(r-4.6-arm64)microseq_2.2.0.tar.gz(r-4.6-x86_64)
microseq_2.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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:

cpp

5.44 score 4 stars 4 packages 144 scripts 785 downloads 24 exports 19 dependencies

Last updated from:06f12242fc. Checks:13 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	WARNING	101
linux-devel-x86_64	WARNING	130
source / vignettes	OK	201
linux-release-arm64	WARNING	96
linux-release-x86_64	WARNING	122
macos-release-arm64	WARNING	152
macos-release-x86_64	WARNING	226
macos-oldrel-arm64	WARNING	180
macos-oldrel-x86_64	WARNING	235
windows-devel-arm64	WARNING	331
windows-devel-x86_64	WARNING	148
windows-release-arm64	WARNING	345
windows-release-x86_64	WARNING	101
windows-oldrel-x86_64	WARNING	104
wasm-release	OK	90

Exports:backTranslate ctranslate 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 generics glue lifecycle magrittr pillar pkgconfig R6 Rcpp rlang stringi stringr tibble tidyselect utf8 vctrs withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Replace amino acids with codons	backTranslate
Translating codons into a single letter alphabet	ctranslate
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
Basic Biological Sequence Analysis	microseq
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