- recipe bioconductor-strandcheckr
Calculate strandness information of a bam file
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/strandCheckR.html
- License:
GPL (>= 2)
- Recipe:
This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering.
- package bioconductor-strandcheckr¶
-
- Versions:
1.16.0-0
,1.12.0-0
,1.10.0-0
,1.8.0-1
,1.8.0-0
,1.6.0-0
,1.4.0-0
,1.2.0-1
,1.0.0-0
- Depends:
bioconductor-biocgenerics
>=0.44.0,<0.45.0
bioconductor-genomeinfodb
>=1.34.0,<1.35.0
bioconductor-genomicalignments
>=1.34.0,<1.35.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-iranges
>=2.32.0,<2.33.0
bioconductor-rsamtools
>=2.14.0,<2.15.0
bioconductor-s4vectors
>=0.36.0,<0.37.0
bioconductor-txdb.hsapiens.ucsc.hg38.knowngene
>=3.16.0,<3.17.0
r-base
>=4.2,<4.3.0a0
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-strandcheckr
and update with:
conda update bioconductor-strandcheckr
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-strandcheckr:<tag>
(see bioconductor-strandcheckr/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-strandcheckr/README.html)