recipe bioconductor-icetea

Integrating Cap Enrichment with Transcript Expression Analysis

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/icetea.html

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-icetea/meta.yaml

icetea (Integrating Cap Enrichment with Transcript Expression Analysis) provides functions for end-to-end analysis of multiple 5'-profiling methods such as CAGE, RAMPAGE and MAPCap, beginning from raw reads to detection of transcription start sites using replicates. It also allows performing differential TSS detection between group of samples, therefore, integrating the mRNA cap enrichment information with transcript expression analysis.

package bioconductor-icetea

versions:

1.20.0-0,  1.18.1-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0, 

1.20.0-0,  1.18.1-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-csaw:

>=1.36.0,<1.37.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-shortread:

>=1.60.0,<1.61.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene:

>=3.12.0,<3.13.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

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-icetea

and update with::

   mamba update bioconductor-icetea

To create a new environment, run:

mamba create --name myenvname bioconductor-icetea

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-icetea:<tag>

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

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