- recipe shiba
A versatile method for systematic identification of differential RNA splicing across platforms
- Homepage:
- Documentation:
- License:
MIT / MIT
- Recipe:
A versatile computational method for systematic identification of differential RNA splicing. Shiba/scShiba can quantify and identify differential splicing events from bulk RNA-seq data and single-cell RNA-seq data. Shiba and scShiba are also implemented as Snakemake workflows, SnakeShiba and SnakeScShiba, respectively.
- package shiba¶
- versions:
0.6.1-0- depends bioconductor-deseq2:
>=1.34.0- depends numexpr:
>=2.8.4- depends numpy:
>=1.26.4- depends pandas:
>=1.5.3- depends plotly:
>=5.13.0- depends pysam:
>=0.23.0- depends python:
- depends pyyaml:
>=6.0.2- depends r-base:
>=4.1.3- depends r-data.table:
>=1.14.2- depends r-locfit:
>=1.5_9.4- depends regtools:
>=1.0.0- depends scanpy:
>=1.9.5- depends statsmodels:
>=0.13.5- depends stringtie:
>=3.0.0- depends subread:
>=2.0.8- requirements:
- additional platforms:
Installation
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 shiba and update with:: mamba update shiba
To create a new environment, run:
mamba create --name myenvname shiba
with
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/shiba:<tag> (see `shiba/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/shiba/README.html)
