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

(downloads) docker_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:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

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

Download stats