tkimhofer Goto Github PK

badger

Badge for R Package

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

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

devium

Dynamic Multivariate Data Analysis and Visualization Platform

drake

An R-focused pipeline toolkit for reproducibility and high-performance computing

jekyll

:globe_with_meridians: Jekyll is a blog-aware static site generator in Ruby

jres

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

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

lcmsdata

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.

ml-cheatsheet

Machine learning cheatsheet

ms_pipe

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

msbrowser

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

msfileparserapp

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

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.

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.

packagebuilder

pkgdown

Generate static html documentation for an R package

py_timeseries

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

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).

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)

qnmr

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

rmarkdown-website-examples

Examples of R Markdown Websites

shiny.semantic

Shiny support for powerful Semantic UI library.