recipe bioconductor-sictools

Find SNV/Indel differences between two bam files with near relationship

Homepage:

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

License:

GPL (>=2)

Recipe:

/bioconductor-sictools/meta.yaml

This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.

package bioconductor-sictools

Versions:

1.28.0-0,  1.24.0-2,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-2,  1.20.0-1,  1.20.0-0,  1.18.0-0, 

1.28.0-0,  1.24.0-2,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-2,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.12.0-0

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

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libzlib >=1.2.13,<1.3.0a0

• ncurses >=6.3,<7.0a0

• r-base >=4.2,<4.3.0a0

• r-doparallel >=1.0.8

• r-matrixstats >=0.10.0

• r-plyr >=1.8.3

• r-stringr >=0.6.2

• zlib >=1.2.13,<1.3.0a0

Required By:

Installation

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

conda install bioconductor-sictools

and update with:

conda update bioconductor-sictools

or use the docker container:

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

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

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