{"repo":"epigen/spilterlize_integrate","free":true,"listed":false,"github":"https://github.com/epigen/spilterlize_integrate","clone":"git clone https://github.com/epigen/spilterlize_integrate.git","description":"A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.","language":"R","stars":54,"topics":["atac-seq","batch-effect","chip-seq","count-matrix","dimensionality-reduction","integration","ngs","normalization","rna-seq","bioinformatics"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Sp lit, F ilter , Norma lize and Integrate Next-Generation Sequencing Count Data A Snakemake 8 workflow to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq, ...) including confounding factor analyses and diagnostic visualizations informing and documenting the respective data transformations. This often represents the first analysis after signal processing, critically influencing all downstream analyses. [!NOTE] This workflow adheres to the module specifications of MrBiomics, an effort to augment research by modularizing (biomedical) data science. For more details, instructions, and modules check out the project's repository. ⭐️ Star and share modules you find valuable 📤 - help others discover them, and guide our focus for future work! [!IMPORTANT] If you use this workflow in a publication, please don't forget to give credit to the authors by citing it using this DOI 10.5281/zenodo.8144219. 🖋️ Authors - Stephan Reichl - Christoph Bock 💿 Software This project wouldn't be possible without the following software and their dependencies. Software Reference (DOI) :---: :---: ComplexHeatmap https://doi.org/10.1093/bioinformatics/btw313 CQN https://doi.org/10.1093/biostatistics/kxr054 edgeR https://doi.org/10.1093/bioinformatics/btp616 fastcluster https://doi.org/10.18637/jss.v053.i09 ggplot2 https://ggplot2.tidyverse.org/ li","default_branch":null,"files":null,"tree":[],"storefront":"/r/epigen","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/epigen/spilterlize_integrate/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}