recipe seacr

SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage). It requires R (https://www.r-project.org) and Bedtools (https://bedtools.readthedocs.io/en/latest/) to be available in your path, and it requires bedgraphs from paired-end sequencing as input, which can be generated from read pair BED files (i.e. BED coordinates reflecting the 5' and 3' termini of each read pair) using bedtools genomecov with the "-bg" flag, or alternatively from name-sorted paired-end BAM files as described in "Preparing input bedgraph files" below.

Homepage:

https://github.com/FredHutch/SEACR

License:

https://github.com/FredHutch/SEACR/blob/master/LICENSE

Recipe:

/seacr/meta.yaml

package seacr

(downloads) docker_seacr

versions:

1.3-2,  1.3-1,  1.3-0,  1.1-0

depends r-base:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install seacr

and update with::

   mamba update seacr

To create a new environment, run:

mamba create --name myenvname seacr

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/seacr:<tag>

(see `seacr/tags`_ for valid values for ``<tag>``)

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Link to this page

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