ConsensusClusterPlus

A new clustering algorithm, "binary cut", for clustering similarity matrices of functional terms is implemeted in this package. It also provides functions for visualizing, summarizing and comparing the clusterings.

A comprehensive toolkit that bridges popular Python-based immune repertoire analysis tools and Hugging Face protein language models into the R environment. Provides unified interfaces for TCR distance calculations (tcrdist3), sequence generation probability (OLGA), selection inference (soNNia), clustering (clusTCR), protein embeddings (ESM-2), metaclone discovery (metaclonotypist). Fully compatible with the scRepertoire and immApex ecosystem for single-cell immune repertoire analysis.

Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.

Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.

Subtypes are defined as groups of samples that have distinct molecular and clinical features. Genomic data can be analyzed for discovering patient subtypes, associated with clinical data, especially for survival information. This package is aimed to identify subtypes that are both clinically relevant and biologically meaningful.

iSEEfier provides a set of functionality to quickly and intuitively create, inspect, and combine initial configuration objects. These can be conveniently passed in a straightforward manner to the function call to launch iSEE() with the specified configuration. This package currently works seamlessly with the sets of panels provided by the iSEE and iSEEu packages, but can be extended to accommodate the usage of any custom panel (e.g. from iSEEde, iSEEpathways, or any panel developed independently by the user).