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Data Mining for RNA-seq data: normalization, features selection and classification - DaMiRseq package6 months ago
1 Citing DaMiRseq | 2 Introduction | 3 Data Handling | 4 Two specific supervised machine learning workflows | 5 Normalizing and Adjusting real independent test sets | 6 Adjusting the data: a necessary step? | 7 Check new implementations! | 8 Session Info
DaMiRseq 2.25.0Mattia Chiesa DaMiRseq.Rnw
The PIUMA package - Phenotypes Identification Using Mapper from topological data Analysis10 months ago
Introduction | Motivation | News in Version PIUMA 1.6 | Installation | Scope of this Vignette | The testing dataset | The TDA object | Preparing data for Mapper | TDA Mapper | Nodes Similarity and Enrichment | Network Assessment | Cluster assignment | Geometry-guided Community Mining of TDA Mapper() Graph | Export data for Cytoscape | Session Info | References
PIUMA 1.9.0Laura Ballarini, Alessia Gerbasi, Giuseppe Albi, Arianna Dagliati, Carlo Leonardi, Luca Piacentini, Mattia ChiesaPIUMA_vignette.Rmd
Topology-based Clustering in Seurat10 months ago
Introduction | Installation | Scope of this Vignette | Seurat pbmc3k testing data | PIUMA TDA clustering | Biological Validation: GZMK+ CD8+ T Subset | Quantitative Comparison | Conclusion | Session Info | References
PIUMA 1.9.0Mattia Chiesa, Laura Ballarini, Alessia Gerbasi, Giuseppe Albi, Arianna Dagliati, Luca Piacentini, Carlo LeonardiVignetteSeurat.Rmd