Curator Dashboard

Software package for quantile smoothing and genomic visualization of array data.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Consortium made up of five clinical centers and a data coordinating center. The goal of Teen-LABS is to conduct clinical, epidemiological, and behavioral research in adolescent bariatric surgery, through an observational prospective study protocol. Teen-LABS is an ancillary study to LABS, an observational study of adult bariatric surgery. Research staff, certified in standardized uniform data collection according to the protocol, collect data at pre-operative research visits, at surgery, 30 days and six months post-operative, and annual post-operative research visits at the five participating centers.

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• dkNET
• 11 years ago - submitted by Ko-Wei Lin

Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package that provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.

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• SciCrunch
• 13 years ago - by Anonymous

An organization of various participants and independent efforts representing four major diseases of hereditary nephrolithiasis. The Consortium facilitates cooperative exchange of information and resources among investigators, clinicians, patients, and researchers in order to improve care and outcomes for patients with rare stone diseases. The consortium promotes ready availability of diagnostic testing, pooling of clinical experiences, and availability of tissue banks in order to advance the science.

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• dkNET
• 11 years ago - submitted by Ko-Wei Lin

Software library that implements lightweight suffix array construction algorithm. Provides C API to construct suffix array and Burrows-Wheeler transformed string from given string over constant size alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of the string.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software functions for performing print-run and array level quality assessment.

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• SciCrunch
• 13 years ago - by Anonymous

The ubiquitous genus Alternaria contains many species that are able to invade cereals, oleaginous plants and other crops. Alternaria alternata is considered one of the most important species and can produce several mycotoxins under favourable conditions of temperature and humidity, including the economically important toxins: alternariol (AOH) and alternariol monomethyl ether (AME). The aim of this study was to evaluate the radio-sensitivity of Alternaria alternata spores through different gamma radiation doses. A. alternata growth and the production of AOH and AME were then analyzed. After fungal irradiation with 2 kGy, 5 kGy and 7 kGy, the spores were suspended with sterile distilled water followed by inoculation on wheat grains. The count of the colony-forming units per gram (CFU/g) was performed using Dichloran Rose Bengal Chloramphenicol (DRBC) and Dichloran Chloramphenicol Agar Malt Extract (DCMA); AOH and AME were analyzed using Liquid Chromatography coupled with Mass Spectrometer (LC-MS). Results showed that fungal growth and toxin production increased with the increase of radiation dosage. The implications of these findings in relation to the resistance of A. alternata spores to gamma irradiation are discussed.

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• SciCrunch
• 11 years ago - submitted by karlet danny

Software tool as kmer-based error correction method for whole genome sequencing data. Lighter uses sampling rather than counting to obtain set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package that contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes.

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• SciCrunch
• 13 years ago - by Anonymous

A database which can be used to search for genes critical for a variety of Genito-Urinary system functions and diseases.

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• SciCrunch
• 11 years ago - submitted by Gabrielle Pine

Software pipeline for metagenomic and taxonomical analysis from shotgun sequencing.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software to detect differential expression in microarray and proteomics datasets. Its use has been shown to improve the detection of differentially expressed genes or proteins in these datasets.

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• SciCrunch
• 13 years ago - by Anonymous

MATLAB and Python 3 high-level programming interface for MySQL databases to support data processing chains in science labs. Specifically designed to provide robust and intuitive data model for scientific data processing chains.Used for scientific data pipelines and workflow management.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Protocols and other training materials related to the CLARITY protocol, a technique for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable.

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• SciCrunch
• 14 years ago - by Anonymous

BrainSlices is a repository of annotated high-resolution images of brain tissue.

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• SciCrunch
• 12 years ago - by Anonymous

Software tool for detecting natural selection and recombination in DNA or RNA sequences.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

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• SciCrunch
• 13 years ago - by Anonymous

Cancer research laboratory at the Peter MacCallum Cancer Centre which investigates biomarkers identification, compounds for activity as anti-cancer drugs, and small molecule targeted therapies.

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• SciCrunch
• 14 years ago - by Anonymous