- 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:
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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-sictools/README.html)