Showing 6 of total 6 results (show query)
bryanhanson
ChemoSpec:Exploratory Chemometrics for Spectroscopy
A collection of functions for top-down exploratory data analysis of spectral data including nuclear magnetic resonance (NMR), infrared (IR), Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed for structured experiments, such as metabolomics investigations, where the samples fall into treatment and control groups. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and to help you get usable results quickly. A vignette covering typical operations is available.
Maintained by Bryan A. Hanson. Last updated 1 years ago.
infrarednmrramanspectroscopyultravioletvisiblexrf
59 stars 7.60 score 45 scripts 1 dependents
marekslenker
MorphoTools2:Multivariate Morphometric Analysis
Tools for multivariate analyses of morphological data, wrapped in one package, to make the workflow convenient and fast. Statistical and graphical tools provide a comprehensive framework for checking and manipulating input data, statistical analyses, and visualization of results. Several methods are provided for the analysis of raw data, to make the dataset ready for downstream analyses. Integrated statistical methods include hierarchical classification, principal component analysis, principal coordinates analysis, non-metric multidimensional scaling, and multiple discriminant analyses: canonical, stepwise, and classificatory (linear, quadratic, and the non-parametric k nearest neighbours). The philosophy of the package is described in Šlenker et al. 2022.
Maintained by Marek Šlenker. Last updated 6 months ago.
7 stars 5.02 score 9 scriptsbryanhanson
ChemoSpecUtils:Functions Supporting Packages ChemoSpec and ChemoSpec2D
Functions supporting the common needs of packages 'ChemoSpec' and 'ChemoSpec2D'.
Maintained by Bryan A. Hanson. Last updated 1 years ago.
4 stars 4.43 score 15 scripts 3 dependents
bioc
ddCt:The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.
Maintained by Jitao David Zhang. Last updated 5 months ago.
geneexpressiondifferentialexpressionmicrotitreplateassayqpcr
4.38 score 8 scriptsbioc
SpatialOmicsOverlay:Spatial Overlay for Omic Data from Nanostring GeoMx Data
Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.
Maintained by Maddy Griswold. Last updated 5 months ago.
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsproprietaryplatformsrnaseqspatialdatarepresentationvisualizationopenjdk
4.30 score 8 scripts