Man pages for fchuffar/epimedtools
Useful Tools Allowing Multi-Omics Analysis
| broken_stick | Broken-stick Distribution for 'p' Pieces. |
| check_study | Checking data study properties |
| compute_survival_table | A Function That Computes Survival Table. |
| coxres | A Function That Fits the Cox Regression Model |
| create_study | Study Factory |
| discr | A Function Discretize a Vector of Numeric |
| download_gse_raw_tar | Retrieving _RAW.tar archive from GEO. |
| epimedtools | epimedtools: A package for computating the notorious bar... |
| et_pairs | A Function that Plots Pairs Correpaltion |
| FDR | A Function That Computes de False Discovery Rate. |
| fuse_exp_grp | Fuse two experimental grouping |
| gdc_client_wrapper | gdc-client wrapperChecking data study properties |
| get_cel_filenames | Retrieve Directory's .CEL.gz Files. |
| get_exprin_app | A Function That runs Heatmap App |
| get_fake_study | A Function That Builds a Fake Study. |
| get_gsm | Retrieving .CEL.gz Files from GEO. |
| get_hm_app | A Function That runs Heatmap App |
| get_nbline | A Function That Computes the Number of Line a a Text File |
| get_tcga_exp_grp | Retrieve exp_grp of a given TCGA project from epimeddb |
| intersect_rec | A Function That Perform Intersection Between Sets. |
| longest_common_prefix | A Function That Returns the Longest Common Prefix. |
| m2sd | A Function That Computes 'mean' + 2 * 'sd' on a Numeric... |
| mgetGEO | A memoised version of getGEO |
| monitored_apply | A Monitored Version of 'apply' |
| monitored_sapply | A Monitored Version of 'sapply' |
| mread.csv2 | A memoised version of read.csv2 |
| mreadRDS | A memoised version of readRDS |
| mtgetGEO | An other memoised version of getGEO |
| overview | A Function That Overviews an Experiment Grouping |
| perform_anova | A Function Performing ANOVAs |
| perform_anova_gen | A Function Performs Differential Expression Analysis Based On... |
| plot_bean_expr | A Function That Plots Expression as Beanplots |
| plot_hm | A Function That Plots Heatmaps of Differentialy Expressed... |
| plot_hm2 | A Function That Plots Heatmaps. |
| plot_survival_panel | A Function That Plots Survival Panel |
| plot_survival_panel_simple | A Function That Plots Survival Panel |
| plot_survival_panel_simple2 | A Function That Plots Survival Panel |
| plot_volcano | A Function That Draws a Volcano Plot |
| qc_expr | A Function that Plots Quality Control for an Expression Data... |
| revcomp | A Function That Computes the Reverse Complement of a DNA... |
| scurve | A Function That Plots Survival Curves. |
| simplify_column_names | A Function That Simplifies Column Names. |
| simplify_exp_grp | A Function That Simplifies Expriment Grouping. |
| simplify_factor_names | A Function That Simplifies Factor Names. |
| simplify_sample_names | A Function That Simplifies Sample Names. |
| Study_abstract-class | A Reference Class to represent a multi-omic study. |
| summarize_exp_grp | A Function That Summarizes Expriment Grouping. |
| tcga_explore_data | Exploring data |
| tcga_fum_data | Fuming data |
| tcga_merge_metadata_cart_and_clinicals | Merging metadata cart and clinicals data |
