- recipe bioconductor-umi4cats
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
- Homepage:
https://bioconductor.org/packages/3.14/bioc/html/UMI4Cats.html
- License:
Artistic-2.0
- Recipe:
UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay.
- package bioconductor-umi4cats¶
-
- Versions:
1.4.0-0
,1.2.0-0
,1.0.1-0
,1.0.0-0
- Depends:
bioconductor-annotate
>=1.72.0,<1.73.0
bioconductor-biocfilecache
>=2.2.0,<2.3.0
bioconductor-biocgenerics
>=0.40.0,<0.41.0
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-bsgenome
>=1.62.0,<1.63.0
bioconductor-deseq2
>=1.34.0,<1.35.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-genomicalignments
>=1.30.0,<1.31.0
bioconductor-genomicfeatures
>=1.46.0,<1.47.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-org.hs.eg.db
>=3.14.0,<3.15.0
bioconductor-rbowtie2
>=2.0.0,<2.1.0
bioconductor-regioner
>=1.26.0,<1.27.0
bioconductor-rsamtools
>=2.10.0,<2.11.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-shortread
>=1.52.0,<1.53.0
bioconductor-summarizedexperiment
>=1.24.0,<1.25.0
bioconductor-txdb.hsapiens.ucsc.hg19.knowngene
>=3.2.0,<3.3.0
r-base
>=4.1,<4.2.0a0
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-umi4cats
and update with:
conda update bioconductor-umi4cats
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-umi4cats:<tag>
(see bioconductor-umi4cats/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-umi4cats/README.html)