Introduction to ribiosNGS8 months ago
Introduction | Quick start | Creating an EdgeObject | Running differential gene expression with edgeR | Extracting results | Running with limma-voom | Using the convenience function | Session info
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Introduction to ribiosExpression8 months ago
Introduction | Installation | Quick start | Loading the package | Working with DesignContrast objects | Building from design and contrast matrices | Visualizing the design | Reading and writing expression data | Read an expression matrix into an ExpressionSet | Read GCT/CLS files | Write ExpressionSet to files | Transforming expression data to long format | Probeset summarization | Filtering probesets | Session info
KEGGgraph: Application Examples4 years ago
Introduction | Parse created or edited pathway | Microarray analysis
KEGGgraph: graph approach to KEGG PATHWAY4 years ago
Introduction | Software features | Case studies | Other funtionalities | Acknowledgement | Conclusion | Session Info
Working with the geneset management system GeMS4 years ago
Working with Geneset Management System (GeMS) | Background | Examples | Task 1: show genesets provided by a user | Task 2: insert new genesets to GeMS | Task 3: Remove a geneset | Task 4: Retrieve gene-sets with names | Task 5: Retrieve gene-sets with a certain property | Conclusions | Session information
BioQC Algorithm: Speeding up the Wilcoxon-Mann-Whitney Test6 years ago
Algorithmic improvements | Time benchmark | Conclusion | R Session Info
BioQC-benchmark: Testing Efficiency, Sensitivity and Specificity of BioQC on simulated and real-world data6 years ago
Experiment setup | Sensitivity Benchmark | Mixing Benchmark | Dataset selection and quality control | An example of weighted mixing: heart and jejunum | Pairwise Mixing | Conclusions | Appendix | Comparing BioQC with Principal Component Analysis (PCA) | R Session Info
BioQC-kidney: The kidney expression example6 years ago
Introduction | Importing the data | Running BioQC | Validation with quantitative RT-PCR | Impact of sample removal on differential gene expression analysis | R Session Info
BioQC: Detect tissue heterogeneity in gene expression data6 years ago
Introduction | A dummy example | Using basic data structures | Case study with real dataset | Benchmarking against R implementation | Technical notes | Background matters | Acknowledgement | R Session Info
Comparing the Wilcoxon-Mann-Whitney to alternative statistical tests6 years ago
Computational Performance | R Session Info | References
How to apply the ddCt method8 years ago
The calculated values | Preparation | Choice of the parameters | Results
Using BioQC with signed genesets9 years ago
Introduction | GMT read-in | Expression object construction | Match genes | Perform the analysis | Conclusions | Acknowledgement | R session info
Introduction to the ddCt method for qRT-PCR data analysis: background, algorithm and example11 years ago
RT–PCR | The ddCt Algorithm | Application example | Acknowledgement | Session Info
Introduction to Data Analysis of the Roche xCELLigence System with RTCA Package13 years ago
Introduction to the xCELLigence™System | Basic features of the RTCA package | What to do next? | Session Info
RTCAtransformation: Discussion of transformation methods of RTCA data13 years ago
Introduction | Manipulation | Methods | Session Info
Analyse RT-PCR data with the end-to-end script in ddCt package13 years ago
Introduction | Prerequisites | Using ddCt | Setting parameters | Results | Session Info