Man pages for KSheu/ksheu.library1
KSheu Library1
| bed_to_granges | BED to GRanges |
| calculate_signature_scores | calculate signature scores |
| CCA_from_file | Do Canonical correlation analysis |
| do_kmeans_clustering | Do k-means clustering on data matrix, genes in rownames,... |
| gsea_squared | #GSEA-squared (last mod. 07/2019 ksheu) |
| ICA_from_file | Do Independent components analysis The input matrix X (input... |
| intersect_all | Intersects all lists |
| intersect_doPCA_from_file_and_project_second_dataset | PCA from file and project second dataset |
| intersect_log_doPCA_from_file_and_project_second_dataset | PCA from file and project second dataset after taking log of... |
| log_PCA_from_file | PCA from file after taking log2 |
| make_loadings_gctfile | Format PCA loadings for IGV |
| make_rnk_file | Make .rnk file Input: txt file Output: writes out .rnk file |
| make_scores_file | Makes scores file for IGV |
| NNMF_from_file | Nonnegative matrix factorization |
| PCA_from_file | PCA from file |
| plot_pca | Plot PCA |
| plot_pca_and_save | Plot PCA with save option |
| plot_pca_projection | Plot PCA projection and data points from original PCA |
| plot_pca_projection_all | Plot PCA projection and data points from original PCA with... |
| plot_pca_projection_and_save | Plot PCA projection with save option |
| plot_pca_projection_only | Plot PCA projection only |
| plot_pls | Plot PLS |
| PLSDA_from_file | Partial Least Squares from file |
| PLSDA_from_file_and_predict_second_dataset | Partial Least Squares and predict second dataset |
| PLSR_from_file | Partial Least Squares Regression from file Last mod: 6/17/18,... |
| PLSR_from_file_and_predict_second_dataset | Partial Least Squares and predict second dataset |
| tensor_decomp | Implements tensor factorization methods, Tucker and... |
| varimax_from_file | Varimax rotation from file Last mod: 4/2018, ksheu |
