Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.

This package is desgined to perform statistical analysis to identify statistically significant differentially bound regions between multiple groups of ChIP-seq dataset.

ChIPanalyser is a package to predict and understand TF binding by utilizing a statistical thermodynamic model. The model incorporates 4 main factors thought to drive TF binding: Chromatin State, Binding energy, Number of bound molecules and a scaling factor modulating TF binding affinity. Taken together, ChIPanalyser produces ChIP-like profiles that closely mimic the patterns seens in real ChIP-seq data.

Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster) assembled using data from public repositories.

The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer.

Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.

countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.

In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html.

Datasets to support COPDSexaulDimorphism Package.

This package is for analysis of SILAC labeled complexome profiling data. It uses peptide table in tab-delimited format as an input and produces ready-to-use tables and plots.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Chicken\_probe\_tab.

CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.

Store University of Washington CADD v1.6 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.

An annotation package for use with ChemmineR. This package includes data from DrugBank. DUD data can be downloaded using the "DUD()" function in ChemmineR.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was C\_elegans\_probe\_tab.

Dimension Reduction for Array CGH Data with Minimal Information Loss.

CellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of source-target edges to support arbitrary representations, where each node may or may not have associated genomic data. The output of CellScape is an interactive interface displaying a single cell phylogeny and a cell-by-locus genomic heatmap representing the mutation status in each cell for each locus.

This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format.

Base annotation databases for chicken, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.

This package provides a package containing an environment representing the Celegans.CDF file.

CNViz takes probe, gene, and segment-level log2 copy number ratios and launches a Shiny app to visualize your sample's copy number profile. You can also integrate loss of heterozygosity (LOH) and single nucleotide variant (SNV) data.

Annotation data file for cMAP assembled using data from public data repositories.

Example text-converted C01 image files for use in the CONFESS Bioconductor package.