recipe bioconductor-umi4cats

UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Homepage

https://bioconductor.org/packages/3.13/bioc/html/UMI4Cats.html

License

Artistic-2.0

Recipe

/bioconductor-umi4cats/meta.yaml

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

1.2.0-0,  1.0.1-0,  1.0.0-0

Depends

• bioconductor-annotate >=1.70.0,<1.71.0

• bioconductor-biocfilecache >=2.0.0,<2.1.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-bsgenome >=1.60.0,<1.61.0

• bioconductor-deseq2 >=1.32.0,<1.33.0

• bioconductor-genomeinfodb >=1.28.0,<1.29.0

• bioconductor-genomicalignments >=1.28.0,<1.29.0

• bioconductor-genomicfeatures >=1.44.0,<1.45.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-org.hs.eg.db >=3.13.0,<3.14.0

• bioconductor-rbowtie2 >=1.14.0,<1.15.0

• bioconductor-regioner >=1.24.0,<1.25.0

• bioconductor-rsamtools >=2.8.0,<2.9.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-shortread >=1.50.0,<1.51.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0

• r-base >=4.1,<4.2.0a0

• r-cowplot

• r-dplyr

• r-fda

• r-ggplot2

• r-magick

• r-magrittr

• r-r.utils

• r-rappdirs

• r-rcolorbrewer

• r-reshape2

• r-rlang

• r-scales

• r-stringr

• r-zoo

Required By

Installation

With an activated Bioconda channel (see 2. 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

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