This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the sample by features table of peak intensities in addition to the sample and feature metadata (as a singl<e ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and quantification, feature alignment, missing value imputation and feature annotation. Applications to exhaled air and cell culture in headspace are described in the vignettes and examples. This package was used for data analysis of Gassin Delyle study on adults undergoing invasive mechanical ventilation in the intensive care unit due to severe COVID-19 or non-COVID-19 acute respiratory distress syndrome (ARDS), and permit to identfy four potentiel biomarquers of the infection.

Platform Design Info for The Manufacturer's Name Pae_G1a.

Reads files exported from QX Manager or QuantaSoft containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.

It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.

Platform Design Info for Affymetrix EquGene-1_1-st.

Platform Design Info for Affymetrix RheGene-1_1-st.

Platform Design Info for The Manufacturer's Name X_tropicalis.

Platform Design Info for Affymetrix GenomeWideSNP_6.

Platform Design Info for Affymetrix HuEx-1_0-st-v2.

Platform Design Info for The Manufacturer's Name HG-U133A_2.

Platform Design Info for Affymetrix RJpGene-1_1-st.

This package provides a package for processing protein mass spectrometry data.

Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.

Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.

PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs.

planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. TFs are identified using pre-built hidden Markov model profiles for DNA-binding domains. Then, auxiliary and forbidden domains are used with DNA-binding domains to classify TFs into families and subfamilies (when applicable). Currently, TFs can be classified in 58 different TF families/subfamilies.

This package provides a fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.

Platform Design Info for The Manufacturer's Name HG_U95B.

Platform Design Info for The Manufacturer's Name Chicken.

The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.

Platform Design Info for The Manufacturer's Name RAE230A.

Platform Design Info for The Manufacturer's Name Barley1.

This package provides a package containing an environment representing the PrimeView.cdf file.

The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.