The CGDS-R package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).
CGDS Toolbox provides direct access to cancer genomics data from within the MATLAB environment.
PubTator is a Web-based tool for accelerating manual literature curation (e.g. annotating biological entities and their relationships) through the use of advanced text-mining techniques. As an all-in-one system, PubTator provides one-stop service for annotating PubMed citations.
tmVar is a text-mining approach based on conditional random field (CRF) for extracting a wide range of sequence variants in both protein and gene levels according to a standard sequence variants nomenclature developed by the human genome variation society (HGVS).
GEOquery effectively establishes a bridge between GEO and BioConductor. Easy access to GEO data from BioConductor will likely lead to new analyses of GEO data using novel and rigorous statistical and bioinformatic tools.
dendsort includes functions to optimize ordering of nodes in a dendrogram, without affecting the meaning of the dengrogram. A dengrogram can be sorted based on the average distance of subtrees, or based on the smallest distance value. These sorting methods improve readability and interpretability of tree structure, especially for tasks such as comparison of different disntance measures or linkage types and identification of tight clusters and outliers. As a result, it also introduces more meaningful reordering for a coupled heatmap visualization.