- recipe bioconductor-orfik
Open Reading Frames in Genomics
- Homepage:
- License:
MIT + file LICENSE
- Recipe:
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:
1.14.7-0
,1.14.5-0
,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
>=1.56.0,<1.57.0
bioconductor-biocgenerics
>=0.40.0,<0.41.0
bioconductor-biocparallel
>=1.28.0,<1.29.0
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-bsgenome
>=1.62.0,<1.63.0
bioconductor-deseq2
>=1.34.0,<1.35.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-genomicalignments
>=1.30.0,<1.31.0
bioconductor-genomicfeatures
>=1.46.0,<1.47.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-rsamtools
>=2.10.0,<2.11.0
bioconductor-rtracklayer
>=1.54.0,<1.55.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-summarizedexperiment
>=1.24.0,<1.25.0
libblas
>=3.8.0,<4.0a0
libgcc-ng
>=10.3.0
liblapack
>=3.8.0,<4.0a0
libstdcxx-ng
>=10.3.0
r-base
>=4.1,<4.2.0a0
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-httr
>=1.3.0
r-rcpp
>=1.0.0
r-xml2
>=1.2.0
- Required By:
Installation
With an activated Bioconda channel (see 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¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-orfik/README.html)