fourSynergy is an ensemble algorithm leveraging synergies among the existing 4C-seq algorithms r3C-seq, peakC, r.4cker and fourSig. It uses a weighted voting approach to perform improved interaction calling. fourSynergy supports also differential interaction calling.

Profile maximum likelihood estimation of parameters for flow cytometry data transformations.

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.

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

Per-channel variance stabilization from a collection of flow cytometry samples by Bertlett test for homogeneity of variances. The approach is applicable to microarrays data as well.

This package provides a package to analyze flow cytometric data using gate information to follow population/community dynamics.

This package provides tools for advanced use of the frma package.

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.

F-informed MDS is a new multidimensional scaling-based ordination method that configures data distribution based on the F-statistic (i.e., the ratio of dispersion between groups with shared or differing labels).

This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.

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

makeFeatureDbFromUCSC cannot cope with this track, hence a package.

Store UCSC fitCons fitness consequences scores version 1.01 for the human genome (hg19).

This package provides a user-friendly R package that enables the characterization of each cfDNA fragment overlapping one or multiple mutations of interest, starting from a sequencing file containing aligned reads (BAM file). fRagmentomics supports multiple mutation input formats (e.g., VCF, TSV, or string "chr:pos:ref:alt" representation), accommodates one-based and zero-based genomic conventions, handles mutation representation ambiguities, and accepts any reference file and species in FASTA format. For each cfDNA fragment, fRagmentomics outputs its size, its 3 and 5 sequences, and its mutational status. Optionally, when users set apply_bcftools_norm = TRUE, fRagmentomics invokes the external command-line tool bcftools norm to left-align and normalize variants. If bcftools is not found on the system PATH while this option is enabled, the function errors. The package does not install external software; see the INSTALL file for per-OS instructions.

This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761.

This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.

Enrichment of metabolomics data using KEGG entries. Given a set of affected compounds, FELLA suggests affected reactions, enzymes, modules and pathways using label propagation in a knowledge model network. The resulting subnetwork can be visualised and exported.

Compiled HumanMethylation27 and HumanMethylation450 annotations.

This package provides a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

This package facilitates analysis of both timecourse and steady state flow cytometry experiments. This package was originially developed for quantifying the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers. Functions in this package facilitate the annotation of flow cytometry data with experimental metadata, as often required for publication and general ease-of-reuse. Functions for creating, saving and loading gate sets are also included. In the past, we have typically generated summary statistics for each flowset for each timepoint and then annotated and analyzed these summary statistics. This method loses a great deal of the power that comes from the large amounts of individual cell data generated in flow cytometry, by essentially collapsing this data into a bulk measurement after subsetting. In addition to these summary functions, this package also contains functions to facilitate annotation and analysis of steady-state or time-lapse data utilizing all of the data collected from the thousands of individual cells in each sample.

Perform fast functional enrichment on feature lists (like genes or proteins) using the hypergeometric distribution. Tailored for speed, this package is ideal for interactive platforms such as Shiny. It supports the retrieval of functional data from sources like GO, KEGG, Reactome, Bioplanet and WikiPathways. By downloading and preparing data first, it allows for rapid successive tests on various feature selections without the need for repetitive, time-consuming preparatory steps typical of other packages.

This package provides a Tool for Epistasis Analysis Based on Functional Regression Model.

Data files used by the examples in frma and frmaTools packages.

An R package that tests for enrichment and depletion of user-defined pathways using a Fisher's exact test. The method is designed for versatile pathway annotation formats (eg. gmt, txt, xlsx) to allow the user to run pathway analysis on custom annotations. This package is also integrated with Cytoscape to provide network-based pathway visualization that enhances the interpretability of the results.