openCyto

Extra Credit builds an outline of openCyto's docs the first time your work uses it. Until then, start at the official documentation.

• beadarray Quality assessment and low-level analysis for Illumina BeadArray data
• gage Generally Applicable Gene-set Enrichment for Pathway Analysis
• GenomicDataCommons NIH / NCI Genomic Data Commons Access
• STRINGdb STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis
• InteractionSet Base Classes for Storing Genomic Interaction Data
• arrayQualityMetrics Quality metrics report for microarray data sets
• txdbmaker Tools for making TxDb objects from genomic annotations
• GenomicFiles Distributed computing by file or by range
• ballgown Flexible, isoform-level differential expression analysis
• destiny Creates diffusion maps
• lpsymphony Symphony integer linear programming solver in R
• DSS Dispersion shrinkage for sequencing data