recipe bioconductor-srnadiff

Finding differentially expressed unannotated genomic regions from RNA-seq data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-srnadiff/meta.yaml

srnadiff is a package that finds differently expressed regions from RNA-seq data at base-resolution level without relying on existing annotation. To do so, the package implements the identify-then-annotate methodology that builds on the idea of combining two pipelines approachs differential expressed regions detection and differential expression quantification. It reads BAM files as input, and outputs a list differentially regions, together with the adjusted p-values.

package bioconductor-srnadiff

(downloads) docker_bioconductor-srnadiff

versions:
1.22.0-01.18.0-11.18.0-01.14.0-21.14.0-11.14.0-01.12.2-01.11.0-01.10.1-0

1.22.0-01.18.0-11.18.0-01.14.0-21.14.0-11.14.0-01.12.2-01.11.0-01.10.1-01.10.0-01.8.0-01.6.0-01.4.0-11.2.0-0

depends bioconductor-bayseq:

>=2.36.0,<2.37.0

depends bioconductor-bayseq:

>=2.36.0,<2.37.0a0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0a0

depends bioconductor-biocstyle:

>=2.30.0,<2.31.0

depends bioconductor-biocstyle:

>=2.30.0,<2.31.0a0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0a0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-edger:

>=4.0.2,<4.1.0a0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomeinfodb:

>=1.38.1,<1.39.0a0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0a0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicfeatures:

>=1.54.1,<1.55.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-gviz:

>=1.46.0,<1.47.0

depends bioconductor-gviz:

>=1.46.1,<1.47.0a0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

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 bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-biocmanager:

depends r-devtools:

depends r-rcpp:

>=0.12.8

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-srnadiff

and update with::

   mamba update bioconductor-srnadiff

To create a new environment, run:

mamba create --name myenvname bioconductor-srnadiff

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-srnadiff:<tag>

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

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