recipe bioconductor-cagefightr

CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5’-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.



GPL-3 + file LICENSE



package bioconductor-cagefightr

(downloads) docker_bioconductor-cagefightr


1.2.0-1, 1.2.0-0

Depends bioconductor-biocgenerics


Depends bioconductor-biocparallel


Depends bioconductor-genomeinfodb


Depends bioconductor-genomicfeatures


Depends bioconductor-genomicfiles


Depends bioconductor-genomicinteractions


Depends bioconductor-genomicranges


Depends bioconductor-gviz


Depends bioconductor-interactionset


Depends bioconductor-iranges


Depends bioconductor-rtracklayer


Depends bioconductor-s4vectors


Depends bioconductor-summarizedexperiment


Depends r-assertthat


Depends r-base


Depends r-grr


Depends r-matrix


Depends r-matrix.utils


Depends r-pryr




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

conda install bioconductor-cagefightr

and update with:

conda update bioconductor-cagefightr

or use the docker container:

docker pull<tag>

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