Package: omicverse
OmicVerse is the fundamental package for multi omics included bulk and single cell analysis with Python. For more information, please read our paper:OmicVerse: A single pipeline for exploring the entire transcriptome universeThe original name of the omicverse wasPyomic, 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.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 “interrupted” cells in the original scRNA-seq data.Directory structure.
├──omicverse# Main Python package├──omicverse_guide# Documentation files├──sample# Some test data├──LICENSE
└──README.mdWhere to get itOmicVerse can be installed via conda or pypi and you need to installpytorchat first. Please refer to theinstallation tutorialfor more detailed installation steps and adaptations for different platforms (Windows,LinuxorMac OS).You can useconda install omicverse -c conda-forgeorpip install -U omicversefor installation.UsagePlease checkout the documentations and tutorials atomicverse.readthedocs.io.Data FrameworkpandasanndatanumpymudataReference[1]Scanpywas originally published inGenome biology[2]dynamicTreeCutwas originally published inBioinformatics[3]scDrugwas originally published inComputational and Structural Biotechnology Journal[4]MOFAwas originally published inGenome Biology[5]COSGwas originally published inBriefings in Bioinformatics[6]CellphoneDBwas originally published inNature[7]AUCellwas originally available inBioconductor, and we use the script of Pyscenic to instead.[8]Bulk2Spacewas originally published inNature Communications[9]SCSAwas originally published inFront Genet[10]WGCNAwas originally avaliable inBMC Bioinformatics[11]VIAwas originally published inNature Communications[12]pyDEseq2was originally published inbiorxiv[13]NOCDwas originally avaliable inDeep Learning on Graphs Workshop, KDD[14]SIMBAwas originally published inNature Methods[15]GLUEwas originally published inNature Biotechnology[16]MetaTiMEwas originally published inNature Communications[17]TOSICAwas originally published inNature Communications[18]Harmonywas originally published inNature Methods[19]Scanoramawas originally published inNature Biotechnology[20]Combatwas originally published inbiorxiv[21]TAPEwas originally published inNature Communications[22]SEACellswas originally published inNature Biotechnology[23]Palantirwas originally published inNature Biotechnology[24]STAGATEwas originally published inNature Communications[25]scVIwas originally published inNature Biotechnology[26]MIRAwas originally published inNature Methods[27]Tangramwas originally published inNature Methods[28]STAlignerwas originally published inNature Computational Science[29]CEFCONwas originally published inNature Communications[30]PyComplexHeatmapwas originally published iniMetaIncluded Package not published or preprint[1]Cellulais to provide a toolkit for the exploration of scRNA-seq. These tools perform common single-cell analysis tasks[2]pegasusis a tool for analyzing transcriptomes of millions of single cells. It is a command line tool, a python package and a base for Cloud-based analysis workflows.ContactZehua Zeng (starlitnightly@163.comorzehuazeng@xs.ustb.edu.cn)Lei Hu (hulei@westlake.edu.cn)Developer GuildIf you would like to contribute to omicverse, please refer to ourdeveloper documentation.AcknowledgementsWe would like to thank the following WeChat Official Accounts for promoting Omicverse.OtherLogo made byDesignEvo free logo creator