- recipe bioconductor-inpas
Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
- Homepage:
- License:
GPL (>= 2)
- Recipe:
Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.
- package bioconductor-inpas¶
- versions:
2.10.0-0,2.8.0-0,2.6.0-0,2.2.0-0,2.0.0-0,1.22.0-1,1.22.0-0,1.20.0-0,1.18.0-0,2.10.0-0,2.8.0-0,2.6.0-0,2.2.0-0,2.0.0-0,1.22.0-1,1.22.0-0,1.20.0-0,1.18.0-0,1.16.3-0,1.14.1-0- depends bioconductor-annotationdbi:
>=1.64.0,<1.65.0- depends bioconductor-biobase:
>=2.62.0,<2.63.0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-bsgenome:
>=1.70.0,<1.71.0- depends bioconductor-cleanupdtseq:
>=1.40.0,<1.41.0- depends bioconductor-genomeinfodb:
>=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-plyranges:
>=1.22.0,<1.23.0- depends bioconductor-preprocesscore:
>=1.64.0,<1.65.0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends r-base:
>=4.3,<4.4.0a0- depends r-batchtools:
- depends r-depmixs4:
- depends r-dplyr:
- depends r-flock:
- depends r-future:
- depends r-future.apply:
- depends r-ggplot2:
- depends r-magrittr:
- depends r-parallelly:
- depends r-readr:
- depends r-reshape2:
- depends r-rsqlite:
- 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-inpas and update with:: mamba update bioconductor-inpas
To create a new environment, run:
mamba create --name myenvname bioconductor-inpas
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-inpas:<tag> (see `bioconductor-inpas/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-inpas/README.html)
