This package provides a quality control tool for flow cytometry data based on compositional data analysis.

Feature rankings can be distorted by a single case in the context of high-dimensional data. The cases exerts abnormal influence on feature rankings are called influential points (IPs). The package aims at detecting IPs based on case deletion and quantifies their effects by measuring the rank changes (DOI:10.48550/arXiv.2303.10516). The package applies a novel rank comparing measure using the adaptive weights that stress the top-ranked important features and adjust the weights to ranking properties.

Matching cell populations and building meta-clusters and templates from a collection of FC samples.

This package provides a set of tools for interacting with the Food-Biomarker Ontology (FOBI). A collection of basic manipulation tools for biological significance analysis, graphs, and text mining strategies for annotating nutritional data.

flowGate adds an interactive Shiny app to allow manual GUI-based gating of flow cytometry data in R. Using flowGate, you can draw 1D and 2D span/rectangle gates, quadrant gates, and polygon gates on flow cytometry data by interactively drawing the gates on a plot of your data, rather than by specifying gate coordinates. This package is especially geared toward wet-lab cytometerists looking to take advantage of R for cytometry analysis, without necessarily having a lot of R experience.

FeatSeekR performs unsupervised feature selection using replicated measurements. It iteratively selects features with the highest reproducibility across replicates, after projecting out those dimensions from the data that are spanned by the previously selected features. The selected a set of features has a high replicate reproducibility and a high degree of uniqueness.

This package extends the function of the LiquidAssociation package for genome-wide application. It integrates a screening method into the LA analysis to reduce the number of triplets to be examined for a high LA value and provides code for use in subsequent significance analyses.

This package is intended to fill the role of conventional cytometry pre-processing software, for spectral decomposition, transformation, visualization and cleanup, and to aid further downstream analyses, such as with DepecheR, by enabling transformation of flowFrames and flowSets to dataframes. Functions for flowCore-compliant automatic 1D-gating/filtering are in the pipe line. The package name has been chosen both as it will deal with spectral cytometry and as it will hopefully give the user a nice pair of spectacles through which to view their data.

CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center.

Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.

This package provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.

This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.

Fragment-level analysis of gas chromatography-massspectrometry metabolomics data.

FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting.

Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees.

The funOmics package ggregates or summarizes omics data into higher level functional representations such as GO terms gene sets or KEGG metabolic pathways. The aggregated data matrix represents functional activity scores that facilitate the analysis of functional molecular sets while allowing to reduce dimensionality and provide easier and faster biological interpretations. Coordinated functional activity scores can be as informative as single molecules!

FANTOM4 promoters, liftOver'ed from hg18 to hg19, CpGs quantified.

Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts.

This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN.

The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized approach for performing pharmacovigilance analysis.

This package provides a subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate.

makeFeatureDbFromUCSC cannot cope with this track, hence a package.

Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.

(f-divergence Cutoff Index), is to find DEGs in the transcriptomic & proteomic data, and identify DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. fCI provides several advantages compared to existing methods.