Quick start (tl;dr) | Description of padma | Overview of Multiple Factor Analysis | Calculation of individualized pathway deviation scores | Calculation of individualized per-gene deviation scores | Description of built-in datasets | LUAD_subset: D4-GDI signaling pathway in the TCGA-LUAD multi-omic data | msigdb: the MSigDB canonical pathway gene sets | mirtarbase: predicted gene targets of miRNAs | Running padma | Numerical outputs | Graphical outputs | Additional options | Projecting supplementary individuals onto a reference consensus | Missing data imputation | Providing miRNA target predictions | Requesting concise results from padma | FAQ | To-do list and ideas for work in progress | Session Info

Quick start (tl;dr) | Co-expression analysis with coseq | Transformations for normalized profiles with the Gaussian mixture model | Transformations for normalized profiles with K-means | Model selection | Other options | Running coseq | Exploring coseq results | Running coseq on a DESeq2 or edgeR results object | Customizing coseq graphical outputs | coseq FAQs

Introduction | Input data | Use of HTSFilter with varying data types | matrix and data.frame classes | edgeR package pipeline | S3 class DGEExact | S3 class DGELRT | DESeq2 package pipeline: S4 class DESeqDataSet} | Alternative normalization using EDAseq | Session Info | References