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http://icbi.at/software/gpviz/gpviz.shtml
A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants.
Proper citation: GPViz (RRID:SCR_000346) Copy
https://sunnylab.wordpress.com/about/
An antibody supplier that provides a range of human antigens, serum and plasma, and cell culture reagents.
Proper citation: SunnyLab (RRID:SCR_000382) Copy
http://www.bioconductor.org/packages/release/bioc/html/iASeq.html
Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.
Proper citation: iASeq (RRID:SCR_000420) Copy
http://www.massachusetts.edu/index.html
A five-campus public university system in Massachusetts. The system includes four universities, a medical school, and a satellite campus.
Proper citation: University of Massachusetts; Massachusetts; USA (RRID:SCR_000379) Copy
A national university in China with degree programs that include engineering, economics, humanities, law and art at the undergraduate, graduate and doctoral level.
Proper citation: Tianjin University; Tianjin; China (RRID:SCR_000372) Copy
A private, historically black university that offers degree programs at the undergraduate, graduate, doctoral and professional levels. The university has programs that include veterinarian studies, allied health, nursing, education
Proper citation: Tuskegee University; Alabama; USA (RRID:SCR_000373) Copy
A public research university in London with an emphasis in social science degree programs such as law, mathematics, public affairs and international history. The university offers degrees at the undergraduate, graduate and doctoral level.
Proper citation: London School of Economics and Political Science; London; United Kingdom (RRID:SCR_000370) Copy
http://international.tau.ac.il/
A public university in Israel with degree programs in areas such as arts, engineering, humanities, the law and medicine at the undergraduate and graduate level. The university has affiliated but independent schools that focus on specific areas such as music, environmental studies, dentistry, social work, education and neuroscience.
Proper citation: Tel Aviv University; Ramat Aviv; Israel (RRID:SCR_000371) Copy
A supplier of various biochemical products for research in pharmacy and biotechnology as well as the specialty ingredients market. Examples of products include active pharmaceutical ingredients, stem cell therapies, drinking water sanitizers and agriculture services and products.
Proper citation: Lonza (RRID:SCR_000377) Copy
A public university in Australia that offers degree programs in business, law and education as well as health, engineering and the sciences at the undergraduate level. The university also does research at three research institutes and seven research centers which focus on a wide range of business, agricultural, scientific, environmental, and technological issues.
Proper citation: University of Southern Queensland; Queensland; Australia (RRID:SCR_000374) Copy
http://www.bioconductor.org/packages/release/bioc/html/rTANDEM.html
An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.
Proper citation: rTANDEM (RRID:SCR_000409) Copy
A private liberal arts college that offers degrees in social sciences, humanities and natural sciences at the undergraduate level.
Proper citation: Allegheny College; Pennsylvania; USA (RRID:SCR_000369) Copy
https://sites.google.com/site/beckerjeremie/home/nucleofinder
A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes.
Proper citation: NucleoFinder (RRID:SCR_000368) Copy
https://github.com/yongchao/flowPeaks
Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.
Proper citation: flowPeaks (RRID:SCR_000407) Copy
http://saweb2.sabiosciences.com/manuals/GEArrayBrochure.pdf
THIS RESOURCE HAS BEEN DISCONTINUED, documented April 15, 2016. New GEArray Expression Analysis Suite 2.0 was released at Dec 21, 2006, please read Release Notices for details. SABiosciences' GEArray Analysis Suite uses advanced Java functionality. In order to experience full functionality of this Portal, the following free programs and upgrades for PC and Macs should be properly installed. PC Environment Downloads Browser compatibility is not an issue on Windows systems, so all operating systems running Windows 98 and above and either Internet explorer or Netscape should be fine. Java 1.4.1 or above is required--this should download automatically upon the first entry into the Portal. If this does not happen, Java 1.5 is available for download from the following URL: Java 1.5 Mac Environment Downloads Browser compatibility is an issue, and Mac Operating Systems prior to Panther are not able to fully take advantage of this Portal's functionality. These programs need to be downloaded and installed in a specific order as follows: Panther 10.3.5 (Operating System), Safari 1.2 (Compatible Internet Browser) and Java 1.4.2 (Java environment). Abstract. INTRODUCTION: Toll-like receptors (TLR) comprehend an emerging family of receptors that recognize pathogen-associated molecular patterns and promote the activation of leukocytes. Surgical trauma and ischemia-reperfusion injury are likely to provide exposure to endogenous ligands for TLR in virtually all kidney transplant recipients. METHODS: Macroarray (GEArray OHS-018.2 Series-Superarray) analyses of 128 genes involved in TLR signaling pathway were performed in nephrectomy samples of patients with chronic allograft nephropathy (CAN) and acute rejection (AR, vascular and non vascular). The analysis of each membrane was performed by GEArray Expression Analysis Suite 2.0. RESULTS: Macroarray profile identified a gene expression signature that could discriminate CAN and AR. Three genes were significantly expressed between CAN and vascular AR: Pellino 2; IL 8 and UBE2V1. In relation to vascular and non-vascular AR, there were only two genes with statistical significance: IL-6 and IRAK-3. CONCLUSION: Vascular and non-vascular AR and CAN showed different expression of a few genes in TLR pathway. The analysis of nephrectomy showed that activation of TLR pathway is present in AR and CAN. Sponsor. This work was supported by the inconditional grant from Fundao de Amparo a Pesquisa do Estado de So Paulo (FAPESP, 04/08311-6), from Conselho Nacional de Pesquisa e Desenvolvimento (CNPq) and from Fundao Osvaldo Ramos.
Proper citation: GEArray Expression Analysis Suite 2.0 (RRID:SCR_000282) Copy
http://proteinprophet.sourceforge.net/
Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.
Proper citation: ProteinProphet (RRID:SCR_000286) Copy
https://github.com/mickaelleclercq/mirdup
A software used for the validation of pre-miRNAs predictions as well as predict the final structure of mature miRNA.
Proper citation: MiRdup (RRID:SCR_000316) Copy
http://purl.bioontology.org/ontology/TEO
Ontology for representing events, time, and their relationships.
Proper citation: Time Event Ontology (RRID:SCR_000310) Copy
http://purl.bioontology.org/ontology/VARIO
An ontology for standardized, systematic description of effects, consequences and mechanisms of variations.
Proper citation: Variation Ontology (RRID:SCR_000311) Copy
http://purl.bioontology.org/ontology/SEDI
An ontology for DICOM as used in the SeDI project.
Proper citation: Semantic DICOM Ontology (RRID:SCR_000309) Copy
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