recipe bioconductor-orfik

Open Reading Frames in Genomics

Homepage:

https://bioconductor.org/packages/3.18/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

(downloads) docker_bioconductor-orfik

versions:
1.22.0-01.20.0-01.18.0-11.18.0-01.14.7-11.14.7-01.14.5-01.12.0-01.10.1-0

1.22.0-01.20.0-01.18.0-11.18.0-01.14.7-11.14.7-01.14.5-01.12.0-01.10.1-01.8.1-01.6.0-01.4.1-01.2.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-annotationdbi:

>=1.64.1,<1.65.0a0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0a0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0a0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-bsgenome:

>=1.70.1,<1.71.0a0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0a0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomeinfodb:

>=1.38.1,<1.39.0a0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0a0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicfeatures:

>=1.54.1,<1.55.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0a0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-biomartr:

>=1.0.7,<2.0a0

depends r-cowplot:

>=1.0.0

depends r-curl:

depends r-data.table:

>=1.11.8

depends r-downloader:

depends r-fst:

>=0.9.2

depends r-ggplot2:

>=2.2.1

depends r-gridextra:

>=2.3

depends r-httr:

>=1.3.0

depends r-jsonlite:

depends r-r.utils:

depends r-rcpp:

>=1.0.0

depends r-rcurl:

depends r-withr:

depends r-xml:

depends r-xml2:

>=1.2.0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-orfik

and update with::

   mamba update bioconductor-orfik

To create a new environment, run:

mamba create --name myenvname bioconductor-orfik

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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