recipe bioconductor-scruff

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Homepage:

https://bioconductor.org/packages/3.16/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:

1.16.0-0,  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, 

1.16.0-0,  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 >=1.60.0,<1.61.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-ggbio >=1.46.0,<1.47.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rsubread >=2.12.0,<2.13.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-shortread >=1.56.0,<1.57.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-ggplot2

• r-ggthemes

• r-plyr

• r-scales

• r-stringdist

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-scruff

and update with:

conda update bioconductor-scruff

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-scruff:<tag>

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

Download stats

Link to this page

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