Introduction | Load gene sets | Usage and benchmark with RNA-seq data | Usage and benchmark with proteomics data | Session information | References

Introduction | Using a SLURM workload manager | Resubmitting failed chunks | Accessing remotely stored GSVA ranks | Session information | References

Introduction | Import data | Quality control and pre-processing | Annotate cell types using GSVA | Read gene sets in GMT format | Add gene identifier type metadata | Build parameter object | Calculate GSVA scores | Using GSVA scores to assign cell types | Stability of GSVA scores with sparse data | Benchmarking | Session information | References

Introduction | Import data | Quality control and pre-processing | Spot cell-type annotation using GSVA | Benchmarking | Session information | References

Quick start | Introduction | Overview of the GSVA functionality | Gene set definitions and containers | Importing gene sets from GMT files | Quantification of pathway activity in bulk microarray and RNA-seq data | Example applications | Molecular signature identification | Differential expression at pathway level | Data exploration at gene level | Running GSVA | Data exploration at pathway level | Interactive web app | Contributing | Session information | References

1 Introduction | 2 Simulating an eQTL network and data from it | 3 Estimating an eQTL network from genetical genomics data | 4 Session information

What is genomic DNA contamination in a RNA-seq experiment | Diagnose gDNA contamination | Strandedness estimation | Remove gDNA contamination | Session information | References

1 Introduction | 2 Simulation of graphs | 3 Simulation of undirected Gaussian GMMs | 4 Simulation of homogeneous mixed GMMs | 5 Simulation of eQTL models of experimental crosses | 6 Session information

What are transposable elements | Currently available methods for quantifying TE expression | TEs annotations | Retrieving and parsing TE annotations | TE expression quantification | Building a parameter object | ERVmap | Telescope | TEtranscripts | Quantifying expression | Accesing expression quantifications and metadata | Session information | References

Getting started | Genomewide position-specific scores | Lossy storage of genomic scores with compressed vectors | Availability and retrieval of genomic scores | Genomic scores as AnnotationHub resources | Building an annotation package from a GScores object | Retrieval of minor allele frequency data | Retrieval of multiple scores per genomic position | Summarization of genomic scores | Annotating variants with genomic scores | Session information | References

Retrieval of the gDNA contaminated RNA-seq data by Li et al. (2022) | Session information

1 Overview | 2 Setting up the analysis | 3 Annotating variants | 4 Filters and cutoffs | 5 Inheritance models | 6 Create a report from the filtered variants | 7 Using the package with parallel execution | 8 Session information

1 Introduction | 2 Preprocessing steps | 3 Reverse engineer a transcriptional regulatory network | 4 Session Information