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Database of the variome of Mycobacterium tuberculosis (Mtb) comprising of over 29,000 single nucleotide variations created from re-analyzed data sets corresponding to over 400 isolates of Mtb. Using a systematic computational pipeline, potential functional variants and drug-resistance associated variants have been annotated. The database has an option to annotate variants from clinical re-sequencing of Mtb.

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• SciCrunch
• 13 years ago - by Anonymous

Software applying a quantitative prediction method to predict the effect of genetic variation using hidden Markov models.

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• SciCrunch
• 13 years ago - by Anonymous

A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that selects genes associated with survival.

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• SciCrunch
• 13 years ago - by Anonymous

Identity-by-descent (IBD) association testing software for genome-wide association study analysis. It requires an IBD detection method such as Beagle FastIBD to run first. GraphIBD then builds upon the IBD information to test if the IBD segments show association to the traits.

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• SciCrunch
• 13 years ago - by Anonymous

A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species.

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• SciCrunch
• 13 years ago - by Anonymous

A software tool for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files.

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• SciCrunch
• 13 years ago - by Anonymous

Clustering software which uses pairwise identity-by-descent (IBD) segments to infer multiple-haplotype IBD clusters. It expands clusters from seed haplotypes by adding qualified neighbors and extends clusters across sliding windows in the genome.

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• SciCrunch
• 13 years ago - by Anonymous

A multithreaded software library that computes statistics on large numbers of datasets, generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions.

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• SciCrunch
• 13 years ago - by Anonymous

Software implementing a supervised classification method for metagenomic samples that takes advantage of the natural structure of microbial community data encoded by phylogenetic trees.

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• SciCrunch
• 13 years ago - by Anonymous

Software for discriminative motif optimization based on perceptron training. It takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. They use the area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. icyou is an internet resource of health-related video clips submitted by users. Health topics covered in videos can range anywhere from infectious diseases to fitness and exercise, with videos generally being shorter than 10 minutes in length. Videos also contain information on treatment and procedures, medical fields, and health politics and policy. These videos may or may not be authored by licensed medical personnel. All videos are searchable, and users can also choose to upload their own healthcare-related videos. In addition to gathering healthcare video from the best sources on the Web and beyond, icyou.com can call on its own award-winning health reporting team to cover the latest issues and trends. Through its parent company Benefitfocus, icyou.com has full access to the Benefitfocus Media Studio, a state-of-the-art HD facility located in Charleston, South Carolina. This studio is the only one of its kind devoted solely to creating healthcare-oriented video content. In it, the Benefitfocus Media team creates up-to-the-minute reports, tutorials, features and more that help illuminate its users about the complexities of the many facets of healthcare.

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• SciCrunch
• 17 years ago - by Anonymous

A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig.

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• SciCrunch
• 13 years ago - by Anonymous

An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that detects somatic single-nucleotide variants using statistical hypothesis testing with multiple testing correction. It uses Fisher's exact test along with multiple testing correction (Benjamini-Hochberg) to find significant differences between allele composition with a specified false discovery rate.

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• SciCrunch
• 12 years ago - by Anonymous

The IETF is an international nonprofit organization whose mission is to provide global educational information, services and support to those affected by essential tremor (ET) and to health care providers, while promoting and funding ET research. Services provided by the IETF include mailing or emailing a free information packet about ET upon request, maintaining an up-to-date listing of physicians specializing in ET, and assisting in forming and maintaining ET support groups. In addition, the IETF conducts several free educational events in cities across the United States every year, and an annual awareness campaign that runs in conjunction with the organization's largest fundraising activity, Tulips for Tremors. Every year, the IETF also funds basic research into the cause(s) of ET. Small grants are awarded to established scientists whose primary interest is tremor disorders. The IETF funds this program in the hope that these scientists will collect sufficient published data to help them qualify for future federal funding that will lead to better treatments and a cure. IETF members receive two copies a year of the member magazine, Tremor Talk and three copies of the research newsletter, The Scoop on Tremor. Articles in both publications are written for the non-medically trained person and discuss recent advances in research, coping techniques and topics of general interest to those with ET. Medical and research articles are written by physicians and researchers who work with patients with ET and/or study ET in laboratories. The International Essential Tremor Foundation is based in Lenexa, Kansas.

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• SciCrunch
• 15 years ago - by Anonymous

A nonprofit organization whose goal is to find better treatments and cures for the movement disorders dystonia and Parkinson's disease. Funding opportunities are available through the collaborative research program between BSDPF and the Michael J. Fox Foundation.

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• SciCrunch
• 14 years ago - by Anonymous

A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely.

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• SciCrunch
• 17 years ago - by Anonymous

Software to manage the conversion of imaging data from one file format and convention to another. It consists of a graphical user interface to visually program the translations, and a data translation engine to read, sort and translate the input files, and write the output files to disk. The data translation engine: (1) Reads metadata from a set of image files on disk to identify the source that produced each file; (2) Groups the image files into user-defined collections using image metadata values; (3) Translates each image file collection by reading metadata and pixel data and mapping the data into the appropriate output file format through a programmable set of connected modules. The Debabeler uses the Java Image I/O Plugin Architecture to read and write a wide variety of common medical image file formats, including ANALYZE, MINC, and most variations of DICOM.

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• SciCrunch
• 17 years ago - by Anonymous

A search program to detect insertions of transposable element from short reads of next generation sequencer.

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• SciCrunch
• 12 years ago - by Anonymous