- recipe bioconductor-qsea
IP-seq data analysis and vizualization
- Homepage:
- License:
GPL-2
- Recipe:
- Links:
biotools: qsea
qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.
- package bioconductor-qsea¶
- versions:
1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.20.0-2,1.20.0-1,1.20.0-0,1.18.0-0,1.16.0-1,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.20.0-2,1.20.0-1,1.20.0-0,1.18.0-0,1.16.0-1,1.16.0-0,1.14.0-0,1.12.0-0,1.10.0-1,1.8.0-0,1.6.0-0,1.4.0-0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-bsgenome:
>=1.70.0,<1.71.0- depends bioconductor-bsgenome:
>=1.70.1,<1.71.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-hmmcopy:
>=1.44.0,<1.45.0- depends bioconductor-hmmcopy:
>=1.44.0,<1.45.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-limma:
>=3.58.0,<3.59.0- depends bioconductor-limma:
>=3.58.1,<3.59.0a0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0a0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends r-base:
>=4.3,<4.4.0a0- depends r-gtools:
- depends r-zoo:
- 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-qsea and update with:: mamba update bioconductor-qsea
To create a new environment, run:
mamba create --name myenvname bioconductor-qsea
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-qsea:<tag> (see `bioconductor-qsea/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-qsea/README.html)
