- recipe chisel
Copy-number Haplotype Inference in Single-cell by Evolutionary Links
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¶
- depends art:
- depends bcftools:
- depends bwa:
- depends gawk:
- depends matplotlib-base:
- depends numpy:
- depends pandas:
- depends python:
- depends samtools:
- depends scipy:
- depends seaborn:
- depends statsmodels:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install chisel and update with:: mamba update chisel
To create a new environment, run:
mamba create --name myenvname chisel
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/chisel:<tag> (see `chisel/tags`_ for valid values for ``<tag>``)