Package Recipe 'shiba'

recipe shiba

A versatile method for systematic identification of differential RNA splicing across platforms

Homepage:: https://github.com/Sika-Zheng-Lab/Shiba
Documentation:: https://sika-zheng-lab.github.io/Shiba
License:: MIT / MIT
Recipe:: /shiba/meta.yaml

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:

0.8.2-0, 0.8.1-1, 0.8.1-0, 0.8.0-0, 0.7.1-0, 0.7.0-0, 0.6.3-0, 0.6.2-0, 0.6.1-0

Depends:

on bioconductor-deseq2 >=1.34.0,<2.0.0
on numexpr >=2.8.4,<3.0.0
on numpy >=1.26.4,<2.0.0
on pandas >=1.5.3,<3.0.0
on plotly >=5.13.0,<6.0.0
on pysam >=0.23.0,<1.0.0
on python >=3.12,<3.13.0a0
on pyyaml >=6.0.2,<7.0.0
on r-base >=4.1.3,<5.0.0
on r-data.table >=1.14.2,<2.0.0
on r-locfit >=1.5_9.4,<2.0.0
on regtools >=1.0.0,<2.0.0
on scanpy >=1.9.5,<2.0.0
on statsmodels >=0.13.5,<1.0.0
on stringtie >=3.0.0,<4.0.0
on subread >=2.0.8,<3.0.0

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 shiba

to add into an existing workspace instead, run:

pixi add shiba

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 shiba

Alternatively, to install into a new environment, run:

conda create -n envname shiba

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/shiba:<tag>

(see shiba/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/shiba/README.html)