Curator Dashboard

An optional module in the Omixon Target application suite for HLA typing using NGS (next-generation sequencing) data that gives high resolution results with whole genome, exome or very targeted DNA data, or with RNA seq data.

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• SciCrunch
• 13 years ago - by Anonymous

A flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. It implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address tasks from preprocessing and quality control to meta-analyses. The user can create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications. In addition to enabling rapid prototyping, the platform is designed to analyze large-datasets in a single-pass fashion in order to minimize memory and intermediate file requirements. The platform supports the widely used BED format to facilitate visualization as well as integration with existing platforms and pipelines such as Galaxy or BioConductor.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Open source viewer / browser software for the SAM / BAM format commonly used in the assembly tasks of Next Generation Sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A next generation sequencing data analysis computer for biologists with or without IT background. It has an easy to-use graphical interface to analyze sequencing data in with only 15 clicks. A range of standard, add-on and custom applications help analyze and visualize data generated by Next Generation Sequencing machines. These are installed on each GenoMiner by default: * Reference assembly * De novo assembly * ChiP-Seq * BLAST * Hybrid de novo assembly * Hybrid reference assembly Add-on applications: * Quality assesment * RNA-Seq * Copy Number Variation (CNV) * Multiple Sequence Alignment * miRNA-Seq * Variant Calling

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• SciCrunch
• 13 years ago - by Anonymous

Software package providing a collection of meta-analysis tools for analysing high throughput experimental data.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer.

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• SciCrunch
• 13 years ago - by Anonymous

Software for obtaining an individualXs HLA class I and II type and expression using standard NGS (Next-generation sequencing) RNA-Seq data. It comprises mapping RNA-Seq reads against a reference database of HLA alleles, determining and reporting HLA type, confidence score and locus-specific expression level.

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• SciCrunch
• 13 years ago - by Anonymous

A fully automated and modular software package for mining sequence data to identify sequences of microbial origin. The pipeline was optimized for analysis of data generated by the Roche/454 next-generation sequencing platform but can be applied to longer sequences (Sanger sequencing data or assembled contigs) as well. Microbial sequences are identified on the basis of BLAST alignments and the taxonomic classification of the reference sequence(s) to which a read is aligned. Viruses are the focal point of VirusHunter as released, but it can be easily modified to generate parallel outputs for bacterial or parasitic species. To date, VirusHunter has been applied to thousands of specimens, including human, animal and environmental samples, resulting in the detection of many known and novel viruses.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool to evaluate de novo genome assemblies with RNA transcripts.

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• SciCrunch
• 13 years ago - by Anonymous

Software program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false positive rate. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations). Note: This software package is no longer supported and information on this page is provided for archival purposes only.

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• SciCrunch
• 13 years ago - by Anonymous

Software to help users work with DICOM files by organizing, managing and analyzing them. Key features: * a smart DICOM viewer with 4 panel display, annotations, arrows, multimodality synchronization, etc... * an export wizard to the most common picture or movie file formats * an export wizard to Microsoft PowerPoint * the most simple and compatible DICOM CD-ROM reader * the most simple and smart DICOM CD-ROM WRITER * an archiving solution with lossless compression of the data * a DICOM creation module to dicomize images from any image source (even video capture) * e-mail or FTP import end export functions (teleradiology) * 16 native localized versions

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• SciCrunch
• 17 years ago - by Anonymous

A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution.

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• SciCrunch
• 13 years ago - by Anonymous

Chinese research university in Beijing, China that offers undergraduate and graduate degree programs in pure and applied sciences, social sciences and humanities, and sciences of management and education.

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• SciCrunch
• 17 years ago - submitted by Stephen Larson

Software to simplify the processing of large rRNA sequence libraries (including single-strand and paired-end reads) obtained through high-throughput sequencing technology. Tools for assembly, quality filtering, taxonomy based analysis and taxonomy independent analysis tools, and tools to convert the data to formats suitable for common ecological and statistical packages are available. For extremely large datasets, command line tools are available.

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• SciCrunch
• 13 years ago - by Anonymous

DNA motif discovery software adapted for ChIP-Seq data. It is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. It does not require truncation of long DNA segments and it is practical for processing up to tens of thousands of data sequences

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Web-based portal and database aggregate of free and open source software for medical imaging. The programs are categorized and placed in a searchable database.

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• SciCrunch
• 17 years ago - by Anonymous

A cloud-based infrastructure for managing, analyzing and sharing genomics datasets.

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• SciCrunch
• 13 years ago - by Anonymous

Analysis pipeline that accurately detects and maps variations that are often missed by standard analysis algorithms. It uses direct de novo read overlap assembly to accurately detect and characterize SNPs (single nucleotide polymorphisms), indels, and SVs (structural variations). The pipeline uses existing Illumina HiSeq data and does not require additional library preparation. The algorithm is optimized for projects with at least 20x coverage per chromosome set (i.e. 40x for diploid).

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 11, 2017. The Third Reviewer is a forum for scientists to share opinions about recently published research. Currently both microbiology and neuroscience papers in different journals are included. Third Reviewer allows anonymous commenting and provides a centralized location for commentary on papers from 11 major neuroscience venues.

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• SciCrunch
• 16 years ago - by Anonymous