recipe bioconductor-riboprofiling

Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/RiboProfiling.html

License:

GPL-3

Recipe:

/bioconductor-riboprofiling/meta.yaml

Links:

biotools: riboprofiling, doi: 10.12688/f1000research.8964.1

Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.

package bioconductor-riboprofiling

Versions:

1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.12.0-1, 

1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.7.1-0,  1.6.0-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-ggbio >=1.46.0,<1.47.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-ggplot2

• r-plyr

• r-reshape2

• r-sqldf

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-riboprofiling

and update with:

conda update bioconductor-riboprofiling

or use the docker container:

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

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

Download stats

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