recipe bioconductor-bcseq

Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/bcSeq.html

License:

GPL-3.0-or-later

Recipe:

/bioconductor-bcseq/meta.yaml

Links:

biotools: bcSeq

This Rcpp-based package implements a highly efficient data structure and algorithm for performing alignment of short reads from CRISPR or shRNA screens to reference barcode library. Sequencing error are considered and matching qualities are evaluated based on Phred scores. A Bayes' classifier is employed to predict the originating barcode of a read. The package supports provision of user-defined probability models for evaluating matching qualities. The package also supports multi-threading.

package bioconductor-bcseq

versions:

1.28.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.16.0-2,  1.16.0-1,  1.16.0-0, 

1.28.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.16.0-2,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-matrix:

depends r-rcpp:

>=0.12.12

requirements:

additional platforms:

linux-aarch64

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 bioconductor-bcseq

and update with::

   mamba update bioconductor-bcseq

To create a new environment, run:

mamba create --name myenvname bioconductor-bcseq

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/bioconductor-bcseq:<tag>

(see `bioconductor-bcseq/tags`_ for valid values for ``<tag>``)

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