bioCancer Package | Pipeline Overview | How to run bioCancer | Portal Panel | Display available Cancer Studies in Table | Studies Panel | Browse the data | Sort | Filters in Table | Global Search | Column filter | Download table as csv file | Side bar Menu | Studies List | Cases and Genetic Profiles for selected study | Gene List Examples | Show Clinical Data in Table | Side bar menu | Select variables to show | Load Clinical Data to Datasets (to Processing Panel) | Show Profiles Data in Table | Load Gene List | Load Profiles to Datasets | Processing Panel | Manage data and state: Load data into bioCancer, Save data to disk, Remove a dataset from memory, or Save/Load the full state of the app | Datasets | Load data | Save data | Save and load state | Remove data from memory | Using commands to load and save data | Show data in table form | Select columns | Filter | Column filters and Search | Visualize data | Plot-type | Box plots | Sub-plots and heat-maps | Line, loess, and jitter | Axis scale | Flip axes | Plot height and width | Customizing plots in R > Report | Create pivot tables to explore your data | Summarize and explore your data | Transform command log | Type | Transform | Create | Recode | Rename | Replace | Clipboard | Normalize | Reorder or remove columns | Reorder or remove levels | Remove missing values | Remove duplicates | Show duplicates | Combine two datasets | Inner join (superheroes, publishers) | Left join (superheroes, publishers) | Right join (superheroes, publishers) | Full join (superheroes, publishers) | Semi join (superheroes, publishers) | Anti join (superheroes, publishers) | Dataset order | Inner join (publishers, superheroes) | Left and Right join (publishers, superheroes) | Full join (publishers, superheroes) | Semi join (publishers, superheroes) | Anti join (publishers, superheroes) | Additional tools to combine datasets (avengers, superheroes) | Bind rows | Bind columns | Intersect | Union | Setdiff | Enrichment Panel | Show multi-Omics Data in Circular Layout | Studies in Wheel | Load Profiles in Datasets | Genes / Diseases / Pathways Classification and clustering | Classification | Plot Clusters | Gene Diseases Association | Function Interaction Network Enrichment | Edges Attributes | Function Interactions (FIs) Type | Use Linkers | Layouts | dot | twopi | neato | circo | Nodes Attributes | From ReactomeFI | From Classifier | mRNA | Studies | From Profiles Data | Legend | Interpretation | References

Introduction | Installation | Suplementary librairies (Not R packages) | dependencies from Bioconductor | Starting Window | Setting Workspace | Main Window | Gene List | Clinical Data | Mutation | Methylation | Profiles | PhenoTest | Examples | GSEA-R | Preprocessing of Exprimental Data | Molecular Signatures DataBase | MSigDB Collection | Study: Uterine Corpus Endometrioid Carcinoma (TCGA, Nature 2013) | Study: Breast Invasive Carcinoma (TCGA, Provosional) | GSEA-R Result Interpretation | Resolved limits | Linear Modeling of GSEA (GSEAlm) | Results interpretation: | Limitations: | Which Molecular Signature Data base (MSigDB) for gene list | get SubMSigDb for genes list | GSEAlm: Phenotypes into Disease | Disease Free Status (DFS_STATUS) into Prostate Cancer: | Copy Number Cluster Level into Stomach Adenocarcinoma: | GSEAlm: Disease vs Disease} | Breast vs Prostate Cancers: | Genes Classification using mRNA expression (Classification) | Genes vs Diseases (inter-diseases) | Example 1: Breast vs Glioblastoma vs Liver vs Lung Cancers (Figure~@ref(fig:GenesClass)A):} | Example 2: Bladder vs Breast vs Glioblastoma vs Lung vs Ovarian vs Prostate Cancers (Figure~\ref | Genes vs Phenotypes (intra-disease) | Example 1: Genes classification vs OS_STATUS (Living/Deceased) | Example 2: Genes regression vs OS_STATUS (Living/Deceased) | Example 3: Genes classification vs tumor grade (grade1/2/3) | Plots | Example: Association of P53 copy number alteration and mRNA exprssion in glioblastoma | Example: MAP2K2 and ABHD17A mRNA expression (RNA Seq V2 RSEM) levels in Uterine Corpus Endometrioid Carcinoma (TCGA, Nature 2013) | Survival Plots | Kaplan-Meier Curves | Cox proportional Hazards Model | Circos Style | References