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http://pathwaynet.princeton.edu/

Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.

Proper citation: PathwayNet (RRID:SCR_017353) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/peddy

Software package that evaluates correspondence between stated sexes, relationships, and ancestries in pedigree file and those inferred from genotypes in VCF file resulting from human whole genome sequencing or whole exome sequencing studies. Facilitates both automated and interactive, visual detection of sample swaps, poor sequencing quality, and other indicators of sample problems.

Proper citation: peddy (RRID:SCR_017287) Copy   

•   Source: SciCrunch Registry

http://topaz.gatech.edu/GeneMark/

Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark.

Proper citation: GeneMarkS-T (RRID:SCR_017648) Copy   

•   Source: SciCrunch Registry

https://pachterlab.github.io/cgal/

Software tool for computing genome assembly likelihoods.Computes likelihood of reads with respect to assembly and statistical model which can be used as metric for evaluating assemblies. Novel likelihood based approach to assembly assessment in absence of ground truth.

Proper citation: Computing Genome Assembly Likelihoods (RRID:SCR_017624) Copy   

•   Source: SciCrunch Registry

https://github.com/YosefLab/FastProject

Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored.

Proper citation: FastProject (RRID:SCR_017462) Copy   

•   Source: SciCrunch Registry

http://geneontology.org/docs/go-consortium/

Consortium integrates resources from variety of research groups, from model organisms to protein databases to biological research communities actively involved in development and implementation of Gene Ontology. Mission to develop up to date, comprehensive, computational model of biological systems, from molecular level to larger pathways, cellular and organism level systems.

Proper citation: GO Gene Ontology Consortium and Knowledgebase (RRID:SCR_017505) Copy   

•   Source: SciCrunch Registry

https://imputationserver.sph.umich.edu/

Web server to implement whole genotype imputation workflow for efficient parallelization of computationally intensive tasks. Service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity. Used to find haplotype segments and reference panel of sequenced genomes, assign genotypes at untyped markers, improve genome coverage, facilitate comparison and combination of studies that use different marker panels, increase power to detect genetic association, and guide fine mapping.

Proper citation: Michigan Imputation Server (RRID:SCR_017579) Copy   

•   Source: SciCrunch Registry

https://web.expasy.org/protparam/

Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity.

Proper citation: ProtParam Tool (RRID:SCR_018087) Copy   

•   Source: SciCrunch Registry

https://cadd.gs.washington.edu/

Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome.

Proper citation: Combined Annotation Dependent Depletion (RRID:SCR_018393) Copy   

•   Source: SciCrunch Registry

https://reactome.org/

Open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. Core unit of Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form network of biological interactions and are grouped into pathways including classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. External domain expert provides expertise, curator formalizes it into database structure, and external domain expert reviews representation. System of evidence tracking ensures that all assertions are backed up by primary literature. Website is designed to give the user graphical map of known biological processes and pathways that is also an interface. Database and website enable to find, organize, and utilize biological information to support data visualization, integration and analysis.

Proper citation: Reactome Knowledgebase (RRID:SCR_023504) Copy   

•   Source: SciCrunch Registry

https://imputationserver.sph.umich.edu/index.html#!pages/home

Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.

Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy   

•   Source: SciCrunch Registry

https://het.io/search/

Web app that allows users to search for the most important paths connecting any two nodes in Hetionet.

Proper citation: Hetnet Connectivity Search (RRID:SCR_023630) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://thecellmap.org

Web accessible database for visualizing and mining global yeast genetic interaction network. Allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize sub networks, using data driven network layouts in intuitive and interactive manner. Used for storing and visualizing genetic interactions in S. cerevisiae.

Proper citation: TheCellMap (RRID:SCR_018728) Copy   

•   Source: SciCrunch Registry

http://www.regulomedb.org/

Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature.

Proper citation: RegulomeDB (RRID:SCR_017905) Copy   

•   Source: SciCrunch Registry

http://omics.informatics.indiana.edu/AbundantOTU/

Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset.

Proper citation: AbundantOTU+ (RRID:SCR_016527) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/biobakery/biobakery/wiki/Home

Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: biobakery (RRID:SCR_016596) Copy   

•   Source: SciCrunch Registry

http://www.lincsproject.org/

Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center.

Proper citation: LINCS Project (RRID:SCR_016486) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/software/discovar/blog/

Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.

Proper citation: Discovar assembler (RRID:SCR_016755) Copy   

•   Source: SciCrunch Registry