AlpsNMR

This package provides R functions for common pre-procssing steps that are applied on 1H-NMR data. It also provides a function to read the FID signals directly in the Bruker format.

Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment on to the cell-types or individual cells identified in a different experiment.

Seahtrue organizes oxygen consumption and extracellular acidification analysis data from experiments performed on an XF analyzer into structured nested tibbles.This allows for detailed processing of raw data and advanced data visualization and statistics. Seahtrue introduces an open and reproducible way to analyze these XF experiments. It uses file paths to .xlsx files. These .xlsx files are supplied by the userand are generated by the user in the Wave software from Agilent from the assay result files (.asyr). The .xlsx file contains different sheets of important data for the experiment; 1. Assay Information - Details about how the experiment was set up. 2. Rate Data - Information about the OCR and ECAR rates. 3. Raw Data - The original raw data collected during the experiment. 4. Calibration Data - Data related to calibrating the instrument. Seahtrue focuses on getting the specific data needed for analysis. Once this data is extracted, it is prepared for calculations through preprocessing. To make sure everything is accurate, both the initial data and the preprocessed data go through thorough checks.

The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.

The package imports the result of tRNAscan-SE as a GRanges object.

This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.