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Software using a non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp).

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• SciCrunch
• 13 years ago - by Anonymous

A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.

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• SciCrunch
• 13 years ago - by Anonymous

A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data.

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• SciCrunch
• 13 years ago - by Anonymous

A C++ software program for multipoint IBD estimation based on high density SNP genotype data.

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• SciCrunch
• 13 years ago - by Anonymous

Project to study human gene expression and regulation in multiple tissues, providing valuable insights into mechanisms of gene regulation and its disease related perturbations. Genetic variation between individuals will be examined for correlation with differences in gene expression level to identify regions of the genome that influence whether and how much a gene is expressed. Includes initiatives: Novel Statistical Methods for Human Gene Expression Quantitative Trait Loci (eQTL) Analysis ,Laboratory, Data Analysis, and Coordinating Center (LDACC), caHUB Acquisition of Normal Tissues in Support of GTEx Project.

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• SciCrunch
• 13 years ago - by Anonymous

Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation.

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• SciCrunch
• 13 years ago - by Anonymous

An Algorithm based on a BivAriate CUmulative Statistic to identify SNPs significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions.

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• SciCrunch
• 13 years ago - by Anonymous

A software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

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• SciCrunch
• 13 years ago - by Anonymous

A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.

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• SciCrunch
• 13 years ago - by Anonymous

A python software program to identify microsatellite repeat regions based on known polymorphisms identified in a .vcf report after using SAMtools to analyze next-generation sequencing files.

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• SciCrunch
• 13 years ago - by Anonymous

AUTOmated server for predicting functional consequences of amino acid MUTations in protEins.

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• SciCrunch
• 13 years ago - by Anonymous

Database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.

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• SciCrunch
• 17 years ago - by Anonymous

Software that aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions.

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• SciCrunch
• 13 years ago - by Anonymous

Database of ascidian embryonic development at the level of the genome (cis-regulatory sequences, gene expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo (anatomy, morphogenesis). Currently, four organism models are described in Aniseed: Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata.<BR/> This version supports four sets of Ciona intestinalis transcript models: JGI v1.0, KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models. Users can explore their expression profiles during normal or manipulated development, access validated cis-regulatory regions, get the molecular tools used to assay gene function, or all articles related to the function, or regulation of a given gene. Known transcriptional regulators and targets are listed for each gene, as are the gene regulatory networks acting in individual anatomical territories. <BR/> ANISEED is a community tool, and the direct involvement of external contributors is important to optimize the quality of the submitted data. Virtual embryo: The 3D Virtual embryo is available to download in the download section of the website.

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• SciCrunch
• 17 years ago - by Anonymous

The goal of the Genetic Testing Reference Materials Coordination Program (GeT-RM) is to coordinate a self-sustaining community process to improve the availability of appropriate and characterized reference materials for: Quality control (QC), Proficiency testing (PT), Test development &amp; validation, Research. The purpose of this program is: - To help the genetic testing community obtain appropriate and characterized reference materials - To facilitate and coordinate information exchange between users and providers of QC and reference materials - To coordinate efforts for contribution, development, characterization and distribution of reference materials for genetic testing Get-RM provides information about cell lines, DNA, and other kinds of materials that could be used as reference materials for molecular genetic testing. Some of these materials have been characterized by the GeT-RM program and can be divided into three categories: - Genetic Inherited Disease & Pharmacogenetics This section includes information about cell lines, DNA, and other samples that can be used as reference materials for various inherited diseases (including cystic fibrosis, fragile X, Huntington disease, and Ashkenazi Jewish-related diseases), pharmacogenetic loci, and biochemical genetics. The GeT-RM program has confirmed the genotype of many of the genomic DNA samples through testing in multiple clinical genetic laboratories. - Molecular Oncology This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various types of cancers, including leukemia/lymphoma and solid tumors. - Infectious Disease This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various infectious disease pathogens including viruses, bacteria, and protozoa.

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• SciCrunch
• 17 years ago - by Anonymous

This resource gives information about the U.S. Human Genome Project, which was was a 13-year effort to to discover all the estimated 20,000-25,000 human genes and make them accessible for further biological study. The primary project goals were to: - identify all the approximately 20,000-25,000 genes in human DNA, - determine the sequences of the 3 billion chemical base pairs that make up human DNA, - store this information in databases, - improve tools for data analysis, - transfer related technologies to the private sector, and - address the ethical, legal, and social issues (ELSI) that may arise from the project. To help achieve these goals, researchers also studied the genetic makeup of several nonhuman organisms. These include the common human gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse. These parallel studies helped to develop technology and interpret human gene function. Sponsors: The DOE Human Genome Program and the NIH National Human Genome Research Institute (NHGRI) together sponsored the U.S. Human Genome Project.

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• SciCrunch
• 17 years ago - by Anonymous

Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data.

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• SciCrunch
• 13 years ago - by Anonymous