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mzR:parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
Maintained by Steffen Neumann. Last updated 2 months ago.
immunooncologyinfrastructuredataimportproteomicsmetabolomicsmassspectrometryzlibcpp
45 stars 12.77 score 204 scripts 44 dependentsbioc
systemPipeR:systemPipeR: Workflow Environment for Data Analysis and Report Generation
systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.
Maintained by Thomas Girke. Last updated 5 months ago.
geneticsinfrastructuredataimportsequencingrnaseqriboseqchipseqmethylseqsnpgeneexpressioncoveragegenesetenrichmentalignmentqualitycontrolimmunooncologyreportwritingworkflowstepworkflowmanagement
53 stars 11.52 score 344 scripts 3 dependentsbioc
cummeRbund:Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
Maintained by Loyal A. Goff. Last updated 5 months ago.
highthroughputsequencinghighthroughputsequencingdatarnaseqrnaseqdatageneexpressiondifferentialexpressioninfrastructuredataimportdatarepresentationvisualizationbioinformaticsclusteringmultiplecomparisonsqualitycontrol
5.92 score 209 scripts