Curator Dashboard

Software package for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

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• SciCrunch
• 13 years ago - by Anonymous

Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls.

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• SciCrunch
• 13 years ago - by Anonymous

Software library as set of classes for creating statistical genetic programs.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A microarray normalization software (SCAN) to facilitate personalized-medicine workflows with an extension (UPC) that estimates whether a given gene/transcript is active above background levels in a given sample. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. A

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• SciCrunch
• 13 years ago - by Anonymous

A web-interface that enables users to access and download the processed ChIP chip/seq data of nuclear receptors, co-regulators and histone modifications. The web resources also includes processed differential expression data under ligand induction in conditions matched to ChIP_chip/seq data whenever possible. All the ChIP chip/seq peak regions are annotated with enriched HRE and co-regulator motifs. A list of predicted hormone response genes from integration of nuclear receptor ChIP chip/seq data and differential expression data is also readily available to the users.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software tool as general purpose cluster algorithm for both weighted and unweighted networks. Unsupervised cluster algorithm for graphs based on simulation of stochastic flow in graphs. Cluster algorithm for graphs.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) and combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform.

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• SciCrunch
• 13 years ago - by Anonymous

A national tissue bank that provides management for database purposes, on-line ordering, guidelines, educational programs, policy making and certification of resources.

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• SciCrunch
• 16 years ago - by Anonymous

Software package to remove reads mapping to the lambda phage genome from a fastq file.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source Java library dedicated to semantic measures computation and analysis. Tools based on the SML are also provided through the SML-Toolkit, a command line software giving access to some of the functionalities of the library. The SML and the toolkit can be used to compute semantic similarity and semantic relatedness between semantic elements (e.g. concepts, terms) or entities semantically characterized (e.g. entities defined in a semantic graph, documents annotated by concepts defined in an ontology).

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• SciCrunch
• 14 years ago - by Anonymous

Archival database of cell lines and microbial strains. Maintained by Public Health England, the database is used by scientists to determine the effects of various substances on human cells as well as for controls for diagnostic and antimicrobial susceptibility tests.

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• SciCrunch
• 17 years ago - by Anonymous

Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder.

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• SciCrunch
• 17 years ago - by Anonymous

A statistical software package for comparing metagenomic datasets and clinical data sets comprised of two treatment populations, with each treatment population being made up of multiple samples. It relies on a non-parametric t-test.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software Python program to discover optimal partitioning schemes for DNA sequences.Used for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A multicenter randomized clinical trial that aims to determine the best therapies for people with type 2 diabetes and moderately severe cardiovascular disease. 2368 participants were randomized at 49 sites in 6 countries. All subjects were given intensive medical therapy to control cholesterol and blood pressure and given counseling, if needed, to quit smoking and to lose weight. Beyond that, they compared whether prompt revascularization, either bypass surgery or angioplasty, e.g. stents, was more effective than medical therapy alone. At the same time, they also looked at which of two diabetes treatment strategies resulted in better outcomes����??insulin-providing versus insulin-sensitizing - that is, increasing the amount of insulin or making the insulin work better. Only patients with known type 2 diabetes and heart disease that could be treated appropriately with a revascularization OR medical therapy alone were eligible for the trial. Patients entered the study between January 2001 ����?? March 2005 and were followed for an average of five years. When a patient entered the study, physicians first decided whether that patient should receive stenting or bypass surgery. The patient then received their randomization assignment. All patients were treated in BARI 2D for both their diabetes and heart disease, as well as other risk factors that might effect those diseases, regardless of which group they were in. Diabetes-specific complications including retinopathy, nephropathy, neuropathy, and peripheral vascular disease were monitored regularly. Tests, blood samples, urine samples, and treatment cost data were obtained periodically through the trial and examined by experts at 7 central laboratories and other research partners. Experts on risk factors routinely oversaw treatments of all patients at 4 central management centers. A panel of independent experts reviewed data every six months to make sure that all patients were receiving safe care.

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• dkNET
• 14 years ago - by Anonymous

Core facility that utilizes a ThermoFisher Cellomics ArrayScan VTI instruments and associated automated cellular analysis software. The High Content Screening (HCS) Core provides a multiplexed functional screening and imaging platform to perform multi-well cell-based assays.

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• SciCrunch
• 10 years ago - by Anonymous

Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Global funder of type 1 diabetes (T1D) research that aims to progressively remove the impact of T1D from people's lives until a world without T1D is achieved. JDRF collaborates with a wide spectrum of partners and is the only organization with the scientific resources, regulatory influence, and a working plan to better treat, prevent, and eventually cure T1D. More than 80 percent of JDRF's expenditures directly support research and research-related education. In 2012 Forbes magazine named JDRF one of its five All-Star charities, citing the organization's efficiency and effectiveness. The organization awards research grants for laboratory and clinical investigations and sponsors a variety of career development and research training programs for new and established investigators. JDRF also sponsors international workshops and conferences for biomedical researchers. Individual chapters offer support groups and other activities for families affected by diabetes.

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• SciCrunch
• 14 years ago - by Anonymous

A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen