- recipe bioconductor-cager
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
- Homepage:
- License:
GPL-3
- Recipe:
- Links:
biotools: cager
The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.
- package bioconductor-cager¶
- versions:
2.12.0-0,2.8.0-0,2.6.0-0,2.4.0-0,2.0.1-0,1.34.0-0,1.32.1-0,1.32.0-0,1.30.0-0,2.12.0-0,2.8.0-0,2.6.0-0,2.4.0-0,2.0.1-0,1.34.0-0,1.32.1-0,1.32.0-0,1.30.0-0,1.28.0-0,1.26.0-1,1.24.0-0,1.22.3-0,1.20.0-0,1.18.1-0,1.16.0-0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0- depends bioconductor-biostrings:
>=2.74.0,<2.75.0- depends bioconductor-bsgenome:
>=1.74.0,<1.75.0- depends bioconductor-cagefightr:
>=1.26.0,<1.27.0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0- depends bioconductor-genomicalignments:
>=1.42.0,<1.43.0- depends bioconductor-genomicfeatures:
>=1.58.0,<1.59.0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0- depends bioconductor-iranges:
>=2.40.0,<2.41.0- depends bioconductor-multiassayexperiment:
>=1.32.0,<1.33.0- depends bioconductor-rsamtools:
>=2.22.0,<2.23.0- depends bioconductor-rtracklayer:
>=1.66.0,<1.67.0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0- depends r-base:
>=4.4,<4.5.0a0- depends r-data.table:
- depends r-formula.tools:
- depends r-ggplot2:
>=2.2.0- depends r-gtools:
- depends r-kernsmooth:
- depends r-memoise:
- depends r-plyr:
- depends r-reshape2:
- depends r-rlang:
- depends r-scales:
- depends r-som:
- depends r-stringdist:
- depends r-stringi:
- depends r-vegan:
- depends r-vgam:
- requirements:
- additional platforms:
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-cager and update with:: mamba update bioconductor-cager
To create a new environment, run:
mamba create --name myenvname bioconductor-cager
with
myenvnamebeing 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-cager:<tag> (see `bioconductor-cager/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-cager/README.html)
