recipe bioconductor-orfik

Open Reading Frames in Genomics

Homepage

https://bioconductor.org/packages/3.13/bioc/html/ORFik.html

License

MIT + file LICENSE

Recipe

/bioconductor-orfik/meta.yaml

R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.

package bioconductor-orfik

Versions

1.12.0-0,  1.10.1-0,  1.8.1-0,  1.6.0-0,  1.4.1-0,  1.2.0-0

Depends

• bioconductor-annotationdbi >=1.54.0,<1.55.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-bsgenome >=1.60.0,<1.61.0

• bioconductor-deseq2 >=1.32.0,<1.33.0

• bioconductor-genomeinfodb >=1.28.0,<1.29.0

• bioconductor-genomicalignments >=1.28.0,<1.29.0

• bioconductor-genomicfeatures >=1.44.0,<1.45.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-rsamtools >=2.8.0,<2.9.0

• bioconductor-rtracklayer >=1.52.0,<1.53.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=9.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=9.3.0

• r-base >=4.1,<4.2.0a0

• r-biomartr

• r-cowplot >=1.0.0

• r-data.table >=1.11.8

• r-fst >=0.9.2

• r-ggally >=1.4.0

• r-ggplot2 >=2.2.1

• r-gridextra >=2.3

• r-r.utils

• r-rcpp >=1.0.0

• r-rcurl

• r-xml2 >=1.2.0

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-orfik

and update with:

conda update bioconductor-orfik

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-orfik:<tag>

(see bioconductor-orfik/tags for valid values for <tag>)

Download stats

Link to this page

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