mpwt is a python package for running Pathway Tools[PathwayToolsarXiv]on multiple genomes using multiprocessing. More precisely, it launches one PathoLogic[Karp2011]process for each organism (PathoLogic and Pathway Tools pathway prediction are described in thisblog entry). This allows to increase the...
Paprica relies on a number of tools and databases developed by other groups. If you cite paprica please be sure to also cite these publications: Barbera, P., Kozlov, A.M., Czech, L., Morel, B., Darriba, D., Flouri, T. and Stamatakis, A., 2019.EPA-ng: Massively Parallel Evoluti...
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We could consider the network crosstalk enrichment tools as the fourth generation. They rely on a network, such as a functional association network like Funcoup8 or STRING9. These networks integrate different experiments from different data types into a single network, providing information about gene...
Using an extension of JavaCyc, Cyclone extracts the BioCyc data model from Pathway Tools and converts it into an XML Schema (Fig. 1a), defining an object model which is Cyclone's pivotal representation. Fig. 1. Information flow in Cyclone from model and data extraction to querying computing...
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S. Single-cell analysis tools for drug discovery and development. Nat. Rev. Drug Discov. 15, 204–216 (2016). Article Google Scholar Meacham, C. E. & Morrison, S. J. Tumour heterogeneity and cancer cell plasticity. Nature 501, 328–337 (2013). Article Google Scholar Hou, W., Ji...
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et al. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. Genome Biol 21, 36 (2020). https://doi.org/10.1186/s13059-020-1949-z 3. PROGENy安装及使用 3.1 安装 截止到本文发布前,PROGENy存储在Bioconductor的版本已经是最新的v1.20版本,和...