recipe chisel

Copy-number Haplotype Inference in Single-cell by Evolutionary Links

Homepage

https://github.com/raphael-group/chisel

License

BSD-3

Recipe

/chisel/meta.yaml

CHISEL is an algorithm to infer allele- and haplotype-specififc copy numbers in individual cells from low-coverage single-cell DNA sequencing data. Specifically, the current implementation of CHISEL has been designed to be diretly applied to ultra-low coverage single-cell DNA sequencing data from 10X Genomics CNV solution, however CHISEL will be adapted to the data generated by any other available technology (e.g. DLP+).

package chisel

Versions

1.1.2-0,  1.1.1-0,  1.1-0,  1.0.0-0,  0.0.5-0,  0.0.4-0,  0.0.2-0

Depends

• art

• bcftools

• bwa

• gawk

• matplotlib-base

• numpy >=1.16.1

• pandas

• python <3

• samtools

• scipy >=1.2.1

• seaborn >=0.7.1,<=0.9.0

• statsmodels <=0.10.1

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install chisel

and update with:

conda update chisel

or use the docker container:

docker pull quay.io/biocontainers/chisel:<tag>

(see chisel/tags for valid values for <tag>)

Download stats

Link to this page

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