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Importing custom data formats16 hours ago
Introduction | Creating GCIMSSample objects | Create the GCIMSDataset | Session info
GCIMS 0.1.1Sergio Ollerimporting-custom-data-formats.Rmd
Introduction to AlpsNMR (older API)2 years ago
Enable parallellization | Data: The MeOH_plasma_extraction dataset | Loading samples | Adding metadata | Interpolation | Plotting samples | Creating interactive plots | Exclude regions | Filter samples | Robust PCA for outlier detection | Baseline removal | Peak detection | Spectra alignment | Normalization | Peak integration | 1. Integration based on peak center and width | 2. Integration based on peak boundaries | Identification | Final thoughts
AlpsNMR 4.15.0AlpsNMR authorsVig01b-introduction-to-alpsnmr-old-api.Rmd
Introduction to AlpsNMR2 years ago
Getting started | Enable parallellization | Data: The MeOH_plasma_extraction dataset | Loading samples | Adding annotations | Phasing | Interpolation | Plotting samples | Exclude regions | Filter samples | Robust PCA for outlier detection | Baseline estimation | Peak detection | Spectra alignment | Normalization | Peak grouping | Session Info:
AlpsNMR 4.15.0AlpsNMR authorsVig01-introduction-to-alpsnmr.Rmd
Introduction to AlpsNMR (older API)2 years ago
Enable parallellization | Data: The MeOH_plasma_extraction dataset | Loading samples | Adding metadata | Interpolation | Plotting samples | Creating interactive plots | Exclude regions | Filter samples | Robust PCA for outlier detection | Baseline removal | Peak detection | Spectra alignment | Normalization | Peak integration | 1. Integration based on peak center and width | 2. Integration based on peak boundaries | Identification | Final thoughts
AlpsNMR 4.11.1AlpsNMR authorsVig01b-introduction-to-alpsnmr-old-api.Rmd
Introduction to AlpsNMR2 years ago
Getting started | Enable parallellization | Data: The MeOH_plasma_extraction dataset | Loading samples | Adding annotations | Phasing | Interpolation | Plotting samples | Exclude regions | Filter samples | Robust PCA for outlier detection | Baseline estimation | Peak detection | Spectra alignment | Normalization | Peak grouping | Session Info:
AlpsNMR 4.11.1AlpsNMR authorsVig01-introduction-to-alpsnmr.Rmd
Introduction to GCIMS2 years ago
Downloading the dataset | Import data | Create a GCIMSDataset object | Filter the retention and drift time of your samples | Smoothing | Decimation | Alignment | Peaks | Clustering | Baseline correction | Peak integration | Build peak table | Imputation | Session Info:
GCIMS 0.1.1GCIMS authorsintroduction-to-gcims.Rmd
Creating a workflow step3 years ago
Introduction | Batch modifying all samples | Example: | Save additional information within each sample | Example | Extracting and aggregating information from samples into the dataset | Extraction | Check that it works: | Aggregation | Session info
GCIMS 0.1.1Sergio Oller Moreno creating-a-workflow-step.Rmd
Using the MassSpecWavelet package3 years ago
Version Info | Overview of MassSpecWavelet | Peak detection by using CWT-based pattern matching | Continuous wavelet transform with Mexican Hat wavelet | Peak identification process | Refine the peak parameter estimation | Future Extension | Acknowledgments | Session Information
MassSpecWavelet 1.79.2Pan Du, Warren A. Kibbe, Simon LinMassSpecWavelet.Rmd
Using the MassSpecWavelet package3 years ago
Version Info | Overview of MassSpecWavelet | Peak detection by using CWT-based pattern matching | Continuous wavelet transform with Mexican Hat wavelet | Peak identification process | Refine the peak parameter estimation | Future Extension | Acknowledgments | Session Information
MassSpecWavelet 1.79.1Pan Du, Warren A. Kibbe, Simon LinMassSpecWavelet.Rmd
Finding local maxima with MassSpecWavelet4 years ago
Introduction | Problems with the classic algorithm | The new local maximum algorithm | Computational cost | Comparison on a real signal | Session Information
MassSpecWavelet 1.79.2Sergio OllerFindingLocalMaxima.Rmd
Finding local maxima with MassSpecWavelet4 years ago
Introduction | Problems with the classic algorithm | The new local maximum algorithm | Computational cost | Comparison on a real signal | Session Information
MassSpecWavelet 1.79.1Sergio OllerFindingLocalMaxima.Rmd
Handling metadata and annotations4 years ago
Getting started | Exploring the sample metadata | Sample annotations | Further annotations | Summary | Session Information
AlpsNMR 4.15.0AlpsNMR authorsVig02-handling-metadata-and-annotations.Rmd
Handling metadata and annotations4 years ago
Getting started | Exploring the sample metadata | Sample annotations | Further annotations | Summary | Session Information
AlpsNMR 4.11.1AlpsNMR authorsVig02-handling-metadata-and-annotations.Rmd
Introduction to condformat9 years ago
Quickstart | Basic syntax | Example:
condformat 0.10.1.9000Sergio Ollerintroduction.Rmd