recipe bioconductor-scruff

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-scruff/meta.yaml

A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.

package bioconductor-scruff

versions:

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.3-0,  1.8.1-0,  1.6.0-0,  1.4.0-0, 

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.3-0,  1.8.1-0,  1.6.0-0,  1.4.0-0,  1.2.4-0,  1.0.1-1,  1.0.1-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-ggbio:

>=1.50.0,<1.51.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rsubread:

>=2.16.0,<2.17.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-shortread:

>=1.60.0,<1.61.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-ggplot2:

depends r-ggthemes:

depends r-parallelly:

depends r-plyr:

depends r-scales:

depends r-stringdist:

requirements:

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-scruff

and update with::

   mamba update bioconductor-scruff

To create a new environment, run:

mamba create --name myenvname bioconductor-scruff

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-scruff:<tag>

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

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Link to this page

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