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http://www.cancerdiagnosis.nci.nih.gov/

National program to improve the diagnosis and assessment of cancer by moving scientific knowledge into clinical practice by coordinating and funding resources and research for the development of innovative in vitro diagnostics, novel diagnostic technologies and appropriate human specimens. The Cancer Diagnosis Program is divided into four branches: Biorepository and Biospecimen Research Branch (BBRB), Diagnostic Biomarkers and Technology Branch (DBTB), Diagnostics Evaluation Branch (DEB), and the Pathology Investigation and Resources Branch (PIRB).

Proper citation: CDP (RRID:SCR_004236) Copy   

•   Source: SciCrunch Registry

http://www.taverna.org.uk/

An open source and domain independent Workflow Management System ����?? a suite of tools used to design and execute scientific workflows and aid in silico experimentation. Taverna Workbench now has support for service sets, offline workflow editing, workflow validation, improved workflow run monitoring, and the pausing and canceling of workflow runs. The command line tool allows you to run workflows outside of the workbench and is available as a stand-alone download or bundled with the Taverna Workbench 2.2.0 download. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick execution of workflows from a terminal. Taverna 2.2.0 includes * Copy/paste, shortcuts, undo/redo, drag and drop * Animated workflow diagram * Remembers added/removed services * Secure Web services support * Secure access to resources on the web * Up-to-date R support * Intermediate values during workflow runs * myExperiment integration * Excel and csv spreadsheet support * Command line tool

Proper citation: Taverna (RRID:SCR_004437) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/rna-star/

Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.

Proper citation: STAR (RRID:SCR_004463) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/QuickGO/

A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services.

Proper citation: QuickGO (RRID:SCR_004608) Copy   

•   Source: SciCrunch Registry

http://www.unc.edu/~yunmli/shotgun.html

Software for short read simulating in order to facilitate sequencing-based study designs.

Proper citation: ShotGun (RRID:SCR_002529) Copy   

•   Source: SciCrunch Registry

http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

Software to identify motifs, conserved regions, in DNA or protein sequences.

Proper citation: Gibbs Motif Sampler (RRID:SCR_002550) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/gap

Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits.

Proper citation: NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) Copy   

•   Source: SciCrunch Registry

http://www.biostars.org/

A question answer forum for scientists, focusing on methods in bioinformatics, computational genomics and biological data analysis. They welcome detailed and specific posts, written clearly and simply.

Proper citation: BioStar (RRID:SCR_002580) Copy   

•   Source: SciCrunch Registry

http://colibread.inria.fr/discosnp/

Software designed for discovering Single Nucleotide Polymorphism (SNP) from raw sets of reads obtained with Next Generation Sequencers (NGS).

Proper citation: discoSnp (RRID:SCR_002612) Copy   

•   Source: SciCrunch Registry

http://cbb.sjtu.edu.cn/~ccwei/pub/software/CTF/CTF.php

Conditional random field (CRF) based transcription factor binding site (TFBS) finding system. The underlying CRF model can integrate features of different sources.

Proper citation: CTF (RRID:SCR_002692) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bio-rainbow/

Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq.

Proper citation: Rainbow (RRID:SCR_002724) Copy   

•   Source: SciCrunch Registry

http://www.pharmgkb.org/

Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.

Proper citation: PharmGKB (RRID:SCR_002689) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/pirs/

Software for de novo data simulation. It uses empirical distribution to reproduce Illumina pair-end reads with real distribution of substitution sequencing errors, quality values and GC%-depth bias.

Proper citation: pIRS (RRID:SCR_002519) Copy   

•   Source: SciCrunch Registry

http://www.geneontology.org/

Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.

Proper citation: Gene Ontology (RRID:SCR_002811) Copy   

•   Source: SciCrunch Registry

http://www.cbil.upenn.edu/RAD

THIS RESOURCE IS NO LONGER IN SERVICE, Documented on March 24, 2014. A resource for gene expression studies, storing highly curated MIAME-compliant studies (i.e. experiments) employing a variety of technologies such as filter arrays, 2-channel microarrays, Affymetrix chips, SAGE, MPSS and RT-PCR. Data were available for querying and downloading based on the MGED ontology, publications or genes. Both public and private studies (the latter viewable only by users having appropriate logins and permissions) were available from this website. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format. RAD is part of a more general Genomics Unified Schema (http://gusdb.org), which includes a richly annotated gene index (http://allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. NOTE: Due to changes in technology and funding, the RAD website is no longer available. RAD as a schema is still very much active and incorporated in the GUS (Genomics Unified Schema) database system used by CBIL (EuPathDB, Beta Cell Genomics) and others. The schema for RAD can be viewed along with the other GUS namespaces through our Schema Browser.

Proper citation: RNA Abundance Database (RRID:SCR_002771) Copy   

•   Source: SciCrunch Registry

http://www.imexconsortium.org/

Interaction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data.

Proper citation: IMEx - The International Molecular Exchange Consortium (RRID:SCR_002805) Copy   

•   Source: SciCrunch Registry

http://andestools.sourceforge.net/

Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses.

Proper citation: ANDES (RRID:SCR_002791) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/R-pbh5

Software library for accessing data in HDF5 files produced by Pacific Biosciences sequencing machines. The R package supports accessing data from: cmp.h5, bas.h5, pls.h5, and trc.h5.

Proper citation: R-pbh5 (RRID:SCR_003026) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/arrayexpress/

International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.

Proper citation: ArrayExpress (RRID:SCR_002964) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/Genbank/

NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.

Proper citation: GenBank (RRID:SCR_002760) Copy   

•   Source: SciCrunch Registry