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Benchmarking - RaMS, MSnBase, Spectra, Arrow, and SQL2 years ago
Intro | Original MSnExp | New onDiskMSnExp infrastructure | Spectra package | RaMS package | tmzML files | Arrow package | SQL(ite) | DuckDB | MS data transformation timings | MS data query timings | Multiple chromatograms | MS object sizing info | Summary
RaMS 1.4.3William Kumlerspeed_size_comparison.Rmd
Introduction to the tmzML file type2 years ago
What is tmzML? | Why tmzML? | Getting started with tmzML documents | Why not tmzML? | tmzML internals
RaMS 1.4.3William Kumler Intro-to-tmzML.Rmd
Minifying files with RaMS2 years ago
RaMS 1.4.3William Kumler Minifying-files-with-RaMS.Rmd
Intro to RaMS2 years ago
Basic RaMS usage | TICs, BPCs, and metadata | Adding a column: MS1 data | Moving along: MSn data | Continuing: chromatograms! | Advanced RaMS usage | Saving space: EICs and rtrange | Speeding things up | Finer control: grabMzmlData, grabMzxmlData | The nitty-gritty details
RaMS 1.4.3William Kumler Intro-to-RaMS.Rmd
Introduction to squallms2 years ago
Setup | Installation | Introduction | Peakpicking with XCMS | Calculating metrics of peak quality (extractChromMetrics) | Labeling | Manual labeling with labelFeatsManual | Lasso labeling with labelFeatsLasso | Building a quality model and removing low-quality peaks | Vignette diagnostics
squallms 1.7.0William Kumlerintro_to_squallms.Rmd
RaMS and friends2 years ago
Standard export to CSV | Fancier export to Excel | Exporting to SQL database | Interfacing with Python via reticulate | R code chunk: | Python code chunk:
RaMS 1.4.3William Kumler RaMS-and-friends.Rmd