bulk-rna-seq-deseq2-analysis-with-omicverse
π―Skillfrom starlitnightly/omicverse
|Performs differential gene expression analysis on bulk RNA-seq data using DESeq2 within the Omicverse computational framework, identifying statistically significant gene expression changes between ...
Part of
starlitnightly/omicverse(24 items)
Installation
pip install -U omicverseSkill Details
Overview
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OmicVerse is the fundamental package for multi omics included bulk ,single cell and spatial RNA-seq analysis with Python. For more information, please read our paper: [OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing](https://www.nature.com/articles/s41467-024-50194-3)
> [!IMPORTANT]
>
> Star Us, You will receive all release notifications from GitHub without any delay \~ βοΈ
>
> If you like OmicVerse and want to support our mission, please consider making a [πdonation](https://ifdian.net/a/starlitnightly) to support our efforts.
`1` [Introduction][docs-feat-provider]
The original name of the omicverse was [Pyomic](https://pypi.org/project/Pyomic/), but we wanted to address a whole universe of transcriptomics, so we changed the name to OmicVerse, it aimed to solve all task in RNA-seq.
> [!NOTE]
> BulkTrajBlend algorithm in OmicVerse that combines Beta-Variational AutoEncoder for deconvolution and graph neural networks for overlapping community discovery to effectively interpolate and restore the continuity of "omission" cells in the original scRNA-seq data.
`2` [Directory structure](#)
````shell
.
βββ omicverse # Main Python package
βββ omicverse_guide # Documentation files
βββ sample # Some test data
βββ LICENSE
βββ README.md
````
`3` [Getting Started ](#)
OmicVerse can be installed via conda or pypi and you need to install pytorch at first. Please refer to the [installation tutorial](https://starlitnightly.github.io/omicverse/Installation_guild/) for more detailed installation steps and adaptations for different platforms (Windows, Linux or Mac OS).
You can use conda install omicverse -c conda-forge or pip install -U omicverse for installation.
Please checkout the documentations and tutorials at [omicverse page](https://starlitnightly.github.io/omicverse/) or [omicverse.readthedocs.io](https://omicverse.readthedocs.io/en/latest/index.html).
`4` [Data Framework and Reference](#)
The omicverse is implemented as an infrastructure based on the following four data structures.
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The table contains the tools have been published