-
recipe
bioconductor-icetea¶ 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.
- Homepage
- License
GPL-3 + file LICENSE
- Recipe
-
package
bioconductor-icetea¶ 
- Versions
1.0.0-0
- Depends bioconductor-biocgenerics
>=0.28.0,<0.29.0
- Depends bioconductor-biocparallel
>=1.16.0,<1.17.0
- Depends bioconductor-biostrings
>=2.50.0,<2.51.0
- Depends bioconductor-csaw
>=1.16.0,<1.17.0
- Depends bioconductor-edger
>=3.24.0,<3.25.0
- Depends bioconductor-genomicalignments
>=1.18.0,<1.19.0
- Depends bioconductor-genomicfeatures
>=1.34.0,<1.35.0
- Depends bioconductor-genomicranges
>=1.34.0,<1.35.0
- Depends bioconductor-iranges
>=2.16.0,<2.17.0
- Depends bioconductor-limma
>=3.38.0,<3.39.0
- Depends bioconductor-rsamtools
>=1.34.0,<1.35.0
- Depends bioconductor-rtracklayer
>=1.42.0,<1.43.0
- Depends bioconductor-s4vectors
>=0.20.0,<0.21.0
- Depends bioconductor-shortread
>=1.40.0,<1.41.0
- Depends bioconductor-summarizedexperiment
>=1.12.0,<1.13.0
- Depends bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene
>=3.4.0,<3.5.0
- Depends bioconductor-variantannotation
>=1.28.0,<1.29.0
- Depends r-base
>=3.5.1,<3.5.2.0a0
- Depends r-ggplot2
- Requirements
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:
[](http://bioconda.github.io/recipes/bioconductor-icetea/README.html)