tkimhofer

msbrowser

An RShiny dashboard for visualisation of mass spectrometry (MS) data and fine-tuning of xcms pre-processing parameters

metabom8

R library for NMR/MS analyses. Workflow includes NMR data import & preprocessing, statistical modelling (PCA, O-PLS), met ID-ing, visualisation (ggplot2, plotly).. Critical functions implemented in C++ using linear algebra packages (Armadillo, Eigen) to improve run-time.

opls

Collection of modelling algorithms for NMR & MS data, including principal components analysis (PLS), (orthogonal) partial least squares (O-PLS, PLS), non-negative least squares regression (NNLSQ). Included are model visualisations based on matplotlib.

jres_cnn

Web-application for 2D NMR peak picking and result visualisation using a Laplacian of Gaussian (LoG) and deep learning (TF Keras) approach - currently under development

Py_TimeSeries

Registration website for event: Time Series with Python (Statistical Society of Australia)

qNMR

XML parser to collect NMR quantification data from Bruker B.I. methods (lipoprotein or metabolite concentrations generated with IVDr experiments)

bconvert

Bruker ms file conversion with baftosql linux docker

BTSimilarity_FastDBSearch

Fast spectral similarity matching based on binary tree distances (Python implementation)

camcheck

RaspberryPi home camera system incl. email altert

MSFileParserApp

Python dashboard for parsing targeted MS files (Skyline) into 2D matrix format, using gunicorn as WSGI server.

pym8

Python version of metabom8 (pronounced "py-mate") for NMR data import and and pre-processing. Significant run time improvements due to parallelisation of selected functions, interactive graphics (matplotlib, plotly).

trp_tq

Targeted MS: Peak deconvolution based on iterative least squares using log-normal distribution and limited-BFGS optimiser (tensorflow, scipy). De-noising and chromatogram consensus peak modelling using autoencoders (tensorflow). Interactive graphics for the identification of the optimal surrogate internal standard.

cleansing

R library for cleaning survey data and automate calculation of univariate summary statistics (formatted as HTML table).

concentr8r

Student project supervision in NMR-based metabolomics: Addressing NMR signal to noise variability of urine samples by adjusting the number of scans at data acquisition stage

jres

R library for reading and visualising J-resolved NMR experiments - spectral import and preprocessing, Rcpp

lcmsData

ml-cheatsheet

Machine learning cheatsheet

ms_pipe

Untargeted LC/GC-MS data processing using xcms (R)

nmr_bulkmag_vizualisation

Teaching - 1D NMR pulse & FID record w two detectors (3D animation, web-link in repo)

NMRalter8r

Student project supervision in NMR-based metabolomics: Addressing NMR signal to noise variability of urine samples by adjusting acquisition parameters using the Jython API of TopSpin

nmrdata

nPYc-Toolbox

The nPYc-Toolbox defines objects for representing, and implements functions to manipulate and display, metabolic profiling datasets.

packagebuilder

pkgdown

Generate static html documentation for an R package

pyms

Python dashboard for mass spectrometry data visualisations: Data import with a Docker image (intel), chromatogram de-noising (autoencoder, Tensorflow), LC-MS feature detection with a nearest neighbour clustering approach (dbscan, scikit-learn)

shiny.semantic

Shiny support for powerful Semantic UI library.

shinyproxy-config-examples

Configuration examples for ShinyProxy

tkimhofer

trp_ms

Data import and QC check for targeted LC-MS assays

tutoral

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