- 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:
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¶
- versions:
1.22.0-0,1.18.0-1,1.18.0-0,1.14.0-2,1.14.0-1,1.14.0-0,1.12.2-0,1.11.0-0,1.10.1-0,1.22.0-0,1.18.0-1,1.18.0-0,1.14.0-2,1.14.0-1,1.14.0-0,1.12.2-0,1.11.0-0,1.10.1-0,1.10.0-0,1.8.0-0,1.6.0-0,1.4.0-1,1.2.0-0- 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
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-srnadiff:<tag> (see `bioconductor-srnadiff/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-srnadiff/README.html)
