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https://support.illumina.com/sequencing/sequencing_instruments/hiseq_1500.html

High-throughput sequencing system. Support of instrument and supply reagents will be provided through February 28th, 2023. Other instruments that support same applications as HiSeq 1500 System are available. Use Sequencing Platform Comparison Tool to find the best instrument for your needs.

Proper citation: Illumina: HiSeq 1500 System (RRID:SCR_018006) Copy   

•   Source: SciCrunch Registry

https://webs.iiitd.edu.in/raghava/coronavir

Web based platform on COVID-19 to maintain predicted diagnostic, drug and vaccine candidates and computational resources on novel coronavirus SARS-CoV-2 and its resulting disease COVID-19. Provides collected and organized information from literature and other resources from internet, links to appropriate literature . Integrated multi-omics repository dedicated to current genomic, proteomic, diagnostic and therapeutic knowledge about coronaviruses.

Proper citation: CoronaVIR (RRID:SCR_018338) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/seqtools

Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites.

Proper citation: Blixem (RRID:SCR_015994) Copy   

•   Source: SciCrunch Registry

http://starbase.sysu.edu.cn/index.php

Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes.

Proper citation: Starbase V2.0 (RRID:SCR_016303) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.mdc-berlin.de/pigx/

Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data.

Proper citation: PiGx (RRID:SCR_016476) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/gatk/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer.

Proper citation: IndelGenotyper (RRID:SCR_016663) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html

Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.

Proper citation: Entrez (RRID:SCR_016640) Copy   

•   Source: SciCrunch Registry

http://portal.brain-map.org/

Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.

Proper citation: Allen Brain Atlas (RRID:SCR_017001) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/GenomicFeatures/

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

Proper citation: GenomicFeatures (RRID:SCR_016960) Copy   

•   Source: SciCrunch Registry

https://omicssimla.sourceforge.io

Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version.

Proper citation: OmicsSIMLA (RRID:SCR_017011) Copy   

•   Source: SciCrunch Registry

https://www.iigm.it/site/index.php?l=ENG

Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience.

Proper citation: Italian Institute for Genomic Medicine; Turin; Italy (RRID:SCR_017062) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/GenomicRanges/

Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.

Proper citation: Genomic Ranges (RRID:SCR_017051) Copy   

•   Source: SciCrunch Registry

http://www.cisreg.ca/cgi-bin/NHR-scan/nhr_scan.cgi

Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications.

Proper citation: Nuclear Hormone Receptor Scan (RRID:SCR_016975) Copy   

•   Source: SciCrunch Registry

http://sonorus.princeton.edu/hefalmp/

HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool.

Proper citation: Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) Copy   

•   Source: SciCrunch Registry

https://www.hsph.harvard.edu/alkes-price/software/

Software application that uses genotyping data from SNP arrays for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data. (entry from Genetic Analysis Software)

Proper citation: Hapmix (RRID:SCR_004203) Copy   

•   Source: SciCrunch Registry

http://www.mknt.hu/sites/default/files/NEPSYBANK_0.doc

The Hungarian Society of Clinical Neurgenetics established a nationwide collaboration for prospective collection of human biological materials and databases from patient with neurological and psychiatric diseases. The basic triangle of the NEPSYBANK is the sample, the information and the study management. The present participants of the NEPSYBANK are the Department of Neurology and Psychiatry of the four Medical Universities (in Budapest, Debrecen, Pecs, Szeged) and the National Institute of Psychiatry and Neurology in Budapest. The NEPSYBANK is a disease based biobank collecting both phenotypical and environmental data and biological materials such as DNA/RNA, whole blood, plasma, cerebral spinal fluid, muscle / nerve / skin biopsy, brain, and fibroblast. The target of the diseases is presently (Phase I): stroke syndromes, dementias, movement disorders, motoneuron diseases, epilepsy, multiple sclerosis, schizophrenia, alcohol addiction. In the near future (Phase II.) it is planned to enlarge the scale with headaches, disorders of the peripheral nerves, disorders of neuromuscular transmission, disorders of skeletal muscle, depression, anxiety. DNA/RNA is usually extracted from whole blood, but occasionally different tissues such as muscle, brain etc. can be used as well. The extracting procedures differ among the institutes, but in all cases the concentration and the quality of the DNA/RNA must be registered in the database. Participating institutional biobanks have committed themselves to follow common quality standards, which provide access to samples after prioritization on scientific grounds only. In every case the following data are registered. 1. General data: main bank categories, age, sex, ethnicity, body height, body weight, economic stats, education, type of place of living, marital status, birth complications, alcohol, drugs, smoking. 2. Sample properties (sample ID, type of sample, date of extraction, concentration, and level of purity). General patient data as blood pressure, heart rate, internal medical status, ECG, additional diseases. Disease specific question e.g. in schizophrenia the diagnosis after DSMIV and ICD 10, detailed diagnostic questions after both classification, detailed psychiatric and neurological status, laboratory findings, rating scales, data of neuroimaging, genetic tests, applied medication (with generic name, dose, duration), adverse drug effects and other treatments. The Biobank Information Management System (BIMS) is responsible for linkage of databases containing information on the individual sample donors. If you want to have samples from the NEPSYBANK an application must be submitted containing the following information: short research plan including aims and study design, ethic application with a positive decision, specific demands regarding the right of disposition, agreements with grant organizations which regulate immaterial property, information about financing (academic grants, support from industry). All participants have the right to withdraw their samples through a simple order.

Proper citation: Hungarian Neurological-Psychiatric Biobank (RRID:SCR_003715) Copy   

•   Source: SciCrunch Registry

https://www.stanleygenomics.org/

The Stanley Online Genomics Database uses samples from the Stanley Medical Research Institute (SMRI) Brain Bank. These samples were processed and run on gene expression arrays by a variety of researchers in collaboration with the SMRI. These researchers have performed analyses on their respective studies using a range of analytic approaches. All of the genomic data have been aggregated in this online database, and a consistent set of analyses have been applied to each study. Additionally, a comprehensive set of cross-study analyses have been performed. A thorough collection of gene expression summaries are provided, inclusive of patient demographics, disease subclasses, regulated biological pathways, and functional classifications. Raw data is also available to download. The database is derived from two sets of brain samples, the Stanley Array collection and the Stanley Consortium collection. The Stanley Array collection contains 105 patients, and the Stanley Consortium collection contains 60 patients. Multiple genomic studies have been conducted using these brain samples. From these studies, twelve were selected for inclusion in the database on the basis of number of patients studied, genomic platform used, and data quality. The Consortium collection studies have fewer patients but more diversity in brain regions and array platforms, while the Array collection studies are more homogenous. There are tradeoffs, the Consortium results will be more variable, but findings may be more broadly representative. The collections contain brain samples from subjects in four main groups: Bipolar Schizophrenia, Depression, and Controls Brain regions used in the studies include: Broadman Area 6, Broadman Area 8/9, Broadman Area 10, Broadman Area 46, Cerebellum The 12 studies encompass a range of microarray platforms: Affymetrix HG-U95Av2, Affymetrix HG-U133A, Affymetrix HG-U133 2.0+, Codelink Human 20K, Agilent Human I, Custom cDNA Publications based on any of the clinical or genomic data should credit the Stanley Medical Research Institute, as well as any individual SMRI collaborators whose data is being used. Publications which make use of analytic results/methods in the database should additionally cite Dr. Michael Elashoff. Registration is required to access the data.

Proper citation: Stanley Medical Research Institute Online Genomics Database (RRID:SCR_004859) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/oncotator

A tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. Genomic Annotations, Protein Annotations, and Cancer Annotations are aggregated from many resources. A standalone version of Oncotator is being developed.

Proper citation: Oncotator (RRID:SCR_005183) Copy   

•   Source: SciCrunch Registry

https://sbpdiscovery.org/research/centers/conrad-prebys-center-for-chemical-genomics/

The Conrad Prebys Center for Chemical Genomics (CPCCG) uses advanced screening technologies to identify high level chemical probes that interact with proteins involved in cellular processes. Optimization of these probes using medicinal chemistry and informatics will form the basis of a new generation of medicines. CPCCG is 1 of 4 Comprehensive Centers chosen nationally to be a part of the Molecular Libraries Probe Program (MLP), which established the Molecular Libraries Probe Production Centers Network (MLPCN). The goal is to produce small molecule probes that allow research into health and disease on the cellular level. CPCCG core services span a range of biochemical and cell-based screens for obtaining hits and provide chemistry resources for optimizing hits into probes or drug development. - Full scale screening capabilities and technology which can provide rapid screening on a broad diversity of assays and detection platforms - Several fully-integrated industrial-scale high-throughput screening (HTS) workstations - HTS microscopy/HCS and novel algorithm development for image analysis - Full hit-to-probe chemistry and exploratory pharmacology - Powerful NMR based Chemical Fragment Screening - Highly integrated informatics infrastructure and efficient data mining capabilities - Protein production facility - Cell production facility for scale-up tissue culture The CPCCG Screening Core can screen 96, 384 or 1536 well formats using either biochemical or cell-based assays, and can process over 300,000 wells per day. Total throughput capacity will climb to over 2 million compounds per day following the opening of Burnhams east coast campus in Lake Nona, Florida.

Proper citation: Conrad Prebys Center for Chemical Genomics (RRID:SCR_001687) Copy   

•   Source: SciCrunch Registry

http://www.softberry.com/

Developer of software tools for genomic research focused on computational methods of high throughput biomedical data analysis, including software to support next generation sequencing technologies, transcriptome analysis with RNASeq data, SNP detection and selection of disease specific SNP subsets. Provides custom genome annotation services.

Proper citation: SoftBerry (RRID:SCR_000902) Copy   

•   Source: SciCrunch Registry