BRB-ArrayTools is an integrated software package for the analysis of DNA microarray data.
BRB-ArrayTools contains utilities for processing expression data from multiple experiments, visualization of data, multidimensional scaling, clustering of genes and samples, and classification and prediction of samples. BRB-ArrayTools features drill-down linkage to NCBI databases using clone, GenBank, or UniGene identifiers, and drill-down linkage to the NetAffx database using Probeset ids.
Paxtools is a Java library specially designed for accessing and manipulating data in BioPAX format. The Paxtools Java programming library for BioPAX has been developed to help software developers readily support the import, export and validation of BioPAX-formatted data for various uses in their software . Using Paxtools, a range of BioPAX-compatible software has been developed, including browsers, visualizers, querying engines, editors and converters
PaxtoolsR provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC).
The QUAliFiER package takes advantage of the manual gates to perform an extensive series of statistical quality assessment checks on the gated cell sub-populations while taking into account the structure of the data and the study design to monitor the consistency of population statistics across staining panels, subject, aliquots, channels, or other experimental variables.
FISH Oracle is a web-based software to visualize data from multiple array CGH or SNP array experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (like gene names or karyobands), quick navigation and zooming into interesting regions, and mechanisms to export the visualization into different high quality image formats (PDF, PS, PNG, SVG).
cMonkey identifies relevant conditions in which the genes within a given bicluster (where “biclustering” is condition- or cell-state-specific clustering) are expected to be co-regulated (importantly, in later stages of analysis we use only these conditions to learn TFs and EFs that influence each bicluster). The methods separates the calculation of the score components associated with each datatype into individual calculations but still effectively sample biclusters that optimally satisfy multiple model components (each representing a separate data-type). The method was designed as a preprocessing step for network inference and performed well in comparison to all other methods tested when the trade-off between sensitivity, specificity, and coverage (fraction of conditions and genes included in one or more biclusters) were considered, particularly in context of the other bulk characteristics (cluster size, residual, etc.).
MitoSeek is an open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome.
The Agilent 2100 BioAnalyzer is a nanofluidics device that preforms size fractionation and quantification of small samples of DNA, RNA, or Protein. In addition, the BioAnalyzer is able to preform flow cytometry on small numbers of cells.