Showing 11 of total 11 results (show query)
bioc
MetMashR:Metabolite Mashing with R
A package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the `struct` package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included.
Maintained by Gavin Rhys Lloyd. Last updated 5 months ago.
8.1 match 2 stars 5.81 score 5 scripts
spang-lab
FastRet:Retention Time Prediction in Liquid Chromatography
A framework for predicting retention times in liquid chromatography. Users can train custom models for specific chromatography columns, predict retention times using existing models, or adjust existing models to account for altered experimental conditions. The provided functionalities can be accessed either via the R console or via a graphical user interface. Related work: Bonini et al. (2020) <doi:10.1021/acs.analchem.9b05765>.
Maintained by Tobias Schmidt. Last updated 1 months ago.
retentiontimechromotographylc-msdata-sciencelcmsopenjdk
11.0 match 3.48 score 4 scripts
yonghuidong
RawHummus:Raw Data Quality Control Tool for LC-MS System
Assess LC–MS system performance by visualizing instrument log files and monitoring raw quality control samples within a project.
Maintained by Yonghui Dong. Last updated 2 years ago.
lcmsmetabolomicsorbitrapquality-control
11.0 match 4 stars 3.30 score 2 scripts
cpanse
protViz:Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
Maintained by Christian Panse. Last updated 1 years ago.
funmass-spectrometrypeptide-identificationproteomicsquantificationvisualizationcpp
3.4 match 11 stars 7.88 score 72 scripts 2 dependentsbioc
metaMS:MS-based metabolomics annotation pipeline
MS-based metabolomics data processing and compound annotation pipeline.
Maintained by Yann Guitton. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
3.5 match 15 stars 7.50 score 15 scriptsbioc
MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Maintained by Laurent Gatto. Last updated 3 days ago.
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp
1.8 match 130 stars 12.81 score 772 scripts 36 dependentsbioc
PLPE:Local Pooled Error Test for Differential Expression with Paired High-throughput Data
This package performs tests for paired high-throughput data.
Maintained by Soo-heang Eo. Last updated 5 months ago.
proteomicsmicroarraydifferentialexpression
3.6 match 3.30 score 7 scripts
rwehrens
ptw:Parametric Time Warping
Parametric Time Warping aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). Both warping of peak profiles and of peak lists are supported. A vignette for the latter is contained in the inst/doc directory of the source package - the vignette source can be found on the package github site.
Maintained by Ron Wehrens. Last updated 3 years ago.
1.7 match 8 stars 6.31 score 57 scripts 10 dependents
aariq
chemhelper:Helper Functions For Dealing With GCMS and LCMS data from IonAnalytics
Provides helper functions for parsing data exported from IonAnalytics, calculating retention indecies, and other miscelanous helper functions to assist in data wrangling.
Maintained by Eric Scott. Last updated 2 years ago.
analytical-chemistrymultivariate-analysispls
2.9 match 4 stars 2.41 score 13 scriptsbioc
biodb:biodb, a library and a development framework for connecting to chemical and biological databases
The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.
Maintained by Pierrick Roger. Last updated 5 months ago.
softwareinfrastructuredataimportkeggbiologycheminformaticschemistrydatabasescpp
0.5 match 11 stars 7.85 score 24 scripts 6 dependentsbioc
cosmiq:cosmiq - COmbining Single Masses Into Quantities
cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.
Maintained by David Fischer. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
0.8 match 4.48 score 2 scripts