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http://eyebrowse.cit.nih.gov/

EyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation.

Proper citation: EyeBrowse (RRID:SCR_008000) Copy   

•   Source: SciCrunch Registry

https://cancer.dartmouth.edu/researchers/bioinformatics-resource.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 29,2022. Core to support the implementation of bioinformatics resources for cancer research at Dartmouth. Provides consultation and collaboration for research projects of NCCC members, regular workshops, seminars, services including applied bioinformatics and data mining, computer programming and software engineering, database development and programming and high performance computing and systems administration.

Proper citation: Dartmouth-Hitchcock Bioinformatics Shared Resource (RRID:SCR_009758) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012e-5e87-861a-55da-381e80000000

Core for data driven projects related to basic, clinical and translational research, with a particular emphasis on diabetes. Aims to ensure that researchers take advantage of the most modern and robust methods available in the field of Bioinformatics and Biostatistics.

Proper citation: Harvard Bioinformatics Core at Joslin Diabetes Center (RRID:SCR_009827) Copy   

•   Source: SciCrunch Registry

http://howard.eagle-i.net/i/00000134-a517-1426-bf4c-ca4080000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core for bioinformatics consultation and software access. Laboratory of Molecular Computations and Bioinformatics (LMCB) is a resource facility dedicated to the support of computational biomedical research at Howard University. Provides molecular modeling, molecular dynamics, bioinformatics, and computational quantum chemistry capabilities and support to a variety of research projects at Howard University.

Proper citation: Howard University Center for Computational Biology and Bioinformatics Core Facility (RRID:SCR_009864) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters.

Proper citation: UniGene (RRID:SCR_004405) Copy   

•   Source: SciCrunch Registry

http://platform.cerebellum.neuroinf.jp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Digital research archive for cerebellar research including mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation.

Proper citation: Cerebellar Platform (RRID:SCR_001700) Copy   

•   Source: SciCrunch Registry

http://biobanknetwork.telethon.it/

Network of non profit association of Italian repositories to form catalogue of biospecimens and associated data. Used to collect, process, preserve and distribute biological samples and related clinical data from individuals affected by rare diseases, their relatives or from healthy control individuals, with standards complying with Italian laws and international recommendations. You may browse sample catalogue by diagnosis or use advanced search option. Request for samples is granted only if project is in agreement with TNGB mission and after receiving signed material transfer agreement form.

Proper citation: Telethon Network of Genetic Biobanks (RRID:SCR_004658) Copy   

•   Source: SciCrunch Registry

http://www.sas.com

Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS.

Proper citation: Statistical Analysis System (RRID:SCR_008567) Copy   

•   Source: SciCrunch Registry

https://ascl.net/

Registry for source codes of interest to astronomers and astrophysicists, including solar system astronomers, and lists codes that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. ASCL is indexed by SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net .

Proper citation: Astrophysics Source Code Library (RRID:SCR_017604) Copy   

•   Source: SciCrunch Registry

http://www.broad.mit.edu/mpr/lung

Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.

Proper citation: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=wavethresh

Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.

Proper citation: wavethresh (RRID:SCR_024311) Copy   

•   Source: SciCrunch Registry

http://geno2mp.gs.washington.edu/Geno2MP/#/

Collection of phenotypic profiles for affected individuals and, for unaffected individuals, the phenotypic profile of their affected. Collaborative, shared resource for the human genetics community.

Proper citation: Geno2MP (RRID:SCR_016872) Copy   

•   Source: SciCrunch Registry

http://meme-suite.org/tools/dreme

Software tool to discover short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in sequences compared with shuffled sequences or control sequences (sample output from sequences).

Proper citation: DREME (RRID:SCR_016860) 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://cometa.tigem.it/

Interactive database of miRNA targets and miRNA-regulated gene networks to integrate expression data from hundreds of cellular and tissue conditions. Website includes CoMeTa corank lists and additional targets for all of human miRNAs, their associated pathways resulting from COOL analysis, and miRNA communities with their corresponding enriched functional categories. Website is searchable by miRNA, target gene, or biological function of interest, and represents unique resource to gain insight into miRNA-controlled gene networks and functions.

Proper citation: CoMeTa Website (RRID:SCR_017357) Copy   

•   Source: SciCrunch Registry

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

Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain.

Proper citation: ABA Mouse Brain: Atlas (RRID:SCR_017479) Copy   

•   Source: SciCrunch Registry

https://resistomedb.com

Web tool to explore and visualize Antibiotic Resistance Genes found on Tara Oceans samples. Can be explored by individual ARG or grouped by antibiotic class.

Proper citation: ResistomeDB (RRID:SCR_018305) Copy   

•   Source: SciCrunch Registry

http://casestudies.brain-map.org/celltax

Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing.

Proper citation: CellTax vignette (RRID:SCR_017000) Copy   

•   Source: SciCrunch Registry

https://biosciencecores.umd.edu/proteomics.html

Facility is equipped withThermoFisher Orbitrap Fusion Lumos Tribrid mass spectrometer that is interfaced to Dionex Ultimate3000 RSLCnano HPLC system. Facility also maintains 2 separate data stations dedicated for proteomics data processing, database searching, and generation of reports.

Proper citation: Maryland University Proteomics Core Facility (RRID:SCR_017739) Copy   

•   Source: SciCrunch Registry