mastR: Simplified Customized Design For Differential Expression Analysis5 months ago
Introduction | Installation | Example | 1. Customized contrast matrix | 2. Process data | 3. Results | Visualization | Session Info
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A quick start guide to smartid: Scoring and MARker selection method based on modified Tf-IDf6 months ago
Introduction | Installation | Prepare Data | Labeled Data | Score Samples | Scale and Transform Score | Marker Selection | Un-labeled Data | Compute Overall Score for Gene-set | SessionInfo
mastR: Markers Automated Screening Tool in R1 years ago
Introduction | Installation | Step 1. Build Markers Pool | Generate Markers from Sources | i) Leukocyte gene signature Matrix (LM) | ii) MSigDB | iii) PanglaoDB | iv) Customized gene list | Pool Markers from Sources | Step 2. Signature Identification for Target Group | a) data processing | b) signature selection based on differential expression | c) constrain signature within markers pool | Step 3. Signature Refinement by Background Expression in Tissue | I) data subsetting | II) data filtration | III) markers pool refinement | use CCLE as background data (optional) | IV) combination with Signature | Step 4. Visualization of Final Results | Heatmap | Signature Score Boxplot | Signature Abundance Scatter Plot | Signature GSEA plot | Working with Extension Data Input | Multiple Datasets | Single Cell RNA-sequencing Data | Applications | Score | Deconvolution | Annotation | Session Info