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https://github.com/poruloh/Eagle
Open source software tool for haplotype phasing. Estimates haplotype phase either within genotyped cohort or using phased reference panel.
Proper citation: Eagle (RRID:SCR_017262) Copy
https://github.com/broadinstitute/Drop-seq
Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript.
Proper citation: Drop-seq tools (RRID:SCR_018142) Copy
http://www.broad.mit.edu/node/305
The Connectivity Map aims to generate a detailed map that links gene patterns associated with disease to corresponding patterns produced by drug candidates and a variety of genetic manipulations. The Connectivity Map is the most comprehensive effort yet for using genomics in a drug-discovery framework. It allows researchers to screen compounds against genome-wide disease signatures, rather than a pre-selected set of target genes. Drugs are paired with diseases using sophisticated pattern-matching methods with a high level of resolution and specificity. To build a Connectivity Map, the Broad Institute brings together molecular biologists, genomics specialists, computational scientists, pharmacologists, chemists and chemical biologists, as well as expertise from across the breadth and depth of medicine.Connectivity map is a large public database of signatures of drugs and genes, and pattern-matching tools to detect similarities among these signatures.The parent site for the Broad Institute at MIT has a software library of software applications developed for use in genetic analysis.
Proper citation: National Institute of Mental Health (NIMH) Human Genetics Initiative (RRID:SCR_007436) Copy
https://data.broadinstitute.org/alkesgroup/Eagle/
Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.
Proper citation: Eagle (RRID:SCR_015991) Copy
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