recipe bioconductor-srnadiff

Finding differentially expressed unannotated genomic regions from RNA-seq data

Homepage:

https://bioconductor.org/packages/3.16/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

Versions:

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, 

1.18.0-0,  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 >=2.31.0,<2.32.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-biocstyle >=2.26.0,<2.27.0

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-gviz >=1.42.0,<1.43.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-biocmanager

• r-devtools

• r-rcpp >=0.12.8

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-srnadiff

and update with:

conda update bioconductor-srnadiff

or 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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