recipe bioconductor-icetea

Integrating Cap Enrichment with Transcript Expression Analysis

Homepage

https://bioconductor.org/packages/3.13/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

1.10.0-0,  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 >=0.38.0,<0.39.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-csaw >=1.26.0,<1.27.0

• bioconductor-deseq2 >=1.32.0,<1.33.0

• bioconductor-edger >=3.34.0,<3.35.0

• bioconductor-genomicalignments >=1.28.0,<1.29.0

• bioconductor-genomicfeatures >=1.44.0,<1.45.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-limma >=3.48.0,<3.49.0

• bioconductor-rsamtools >=2.8.0,<2.9.0

• bioconductor-rtracklayer >=1.52.0,<1.53.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-shortread >=1.50.0,<1.51.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.12.0,<3.13.0

• bioconductor-variantannotation >=1.38.0,<1.39.0

• r-base >=4.1,<4.2.0a0

• r-ggplot2

Required By

Installation

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

conda install bioconductor-icetea

and update with:

conda update bioconductor-icetea

or use the docker container:

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

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

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-icetea/README.html)