- recipe chisel
Copy-number Haplotype Inference in Single-cell by Evolutionary Links
- Homepage:
- License:
BSD-3
- Recipe:
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:
1.1.4-0,1.1.3-0,1.1.2-0,1.1.1-0,1.1-0,1.0.0-0,0.0.5-0,0.0.4-0,0.0.2-0- Depends:
on art
on bcftools
on bwa
on gawk
on matplotlib-base
on numpy
>=1.16.1on pandas
on python
<3on samtools
on scipy
>=1.2.1on seaborn
>=0.7.1,<=0.9.0on statsmodels
<=0.10.1
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install chisel
to add into an existing workspace instead, run:
pixi add chisel
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install chisel
Alternatively, to install into a new environment, run:
conda create -n envname chisel
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/chisel:<tag>
(see chisel/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/chisel/README.html)
