- 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:
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-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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-srnadiff/README.html)