recipe bioconductor-simffpe

NGS Read Simulator for FFPE Tissue

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/SimFFPE.html

License:

LGPL-3

Recipe:

/bioconductor-simffpe/meta.yaml

The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRS), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCRs). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples on the whole genome / several chromosomes / large regions.

package bioconductor-simffpe

Versions:

1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• r-base >=4.2,<4.3.0a0

• r-doparallel

• r-dplyr

• r-foreach

• r-truncnorm

Required By:

Installation

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

conda install bioconductor-simffpe

and update with:

conda update bioconductor-simffpe

or use the docker container:

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

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

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