Curator Dashboard

Geospatial software for monitoring and modeling the Earth system. Includes tools for GIS, image processing, surface analysis, vertical applications for land change analysis and earth trends exploration, and more.

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• SciCrunch
• 13 years ago - by Anonymous

The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind.

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• SciCrunch
• 16 years ago - by Anonymous

Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Online portal of the software resources provided by Hanchuan Peng's lab. Program functions include 3D image rendering, MATLAB toolboxs, image annotator, and cell explorer atlas and building tools.

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• SciCrunch
• 16 years ago - by Anonymous

Core Facility provides support for short or long-term projects requiring expertise the analysis of biological datasets. The services provided include the analysis of large-scale datasets (e.g. next-gen sequencing data, microarrays, etc.), the development of customized databases and reusable analysis pipelines, guidance on experimental design, support with technical sections of manuscripts and grants, and training on analysis software packages. All services are charged at our hourly rate.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs.

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• SciCrunch
• 14 years ago - by Anonymous

Core provides the infrastructure for cell-based gain-of-function (ORF, CRISPRa and CRISPRon) and loss-of-functioning (siRN, miRNA, shRNA, CRSIPRko, CRISPRi and CRISPRoff), libraries screening services, starting with assay development and carrying all the way through verification of identified targets. The large scale screens is accomplished via ready-to-use genome-wide or pathway-specific library platforms with choice of arrayed or pooled libraries. The FG core facility is equipped to perform custom CRISPR gene activation, knock-down, knock-out and editing services. We also adopt CRISPR nucleotide base editing technology and offer custom built CRISPR domain libraries. This approach can reveal the specific domain of a target protein interacting with another molecule, such as protein, IncRNA or drug in a native cell cellular environment.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package provides interface to Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. Provides elements of file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species. The system also aims to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data. Sponsors: ArkDB is funded by Biotechnology and Biological Sciences Research Council (BBSRC), UK. Cat, Chicken, Cow, Deer, Duck, Horse, Pig, Quail, Salmon, Sea Bass, Sheep, Turkey, QLT map, Linkage map, RH map, Farm animal, Genome map, Sequence, Mapping

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• SciCrunch
• 17 years ago - by Anonymous

Non-profit dedicated to conducting collaborative research to find cures for human disease, improve quality of life, and educate and train the next-generation of scientists. It is the overarching organization of more than a dozen core facilities that provide various resources in biomedical research.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package provides interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling comprehensive phylogenetic tree for all named species.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software that constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response).

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• SciCrunch
• 12 years ago - by Anonymous

International group of researchers interested in providing standardized gene nomenclature for chicken genes. A Chicken Gene Annotation Tool is available from CGNC-UK which assigns chicken nomenclature based on predicted orthology to human genes. The CGNC-US database includes CGNC-UK information and adds manually biocurated from biocurators and interested contributors. A Human Chicken Ortholog Predictions Search is available. Both resources are part of a united CGNC effort and nomenclature data is shared and co-ordinated between these two resources. They strongly encourage researchers with domain knowledge to participate in this nomenclature effort by requesting a login and providing gene nomenclature for their genes of interest. Please contact them for further information or assistance. The AGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees, including the Chicken Gene Nomenclature Committee (CGNC). The Avian and Chicken nomenclature efforts are co-ordinated and chicken data is shared between these two groups.

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• SciCrunch
• 16 years ago - by Anonymous

Software tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data.

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• SciCrunch
• 14 years ago - by Anonymous

Software tool designed to align expressed DNA sequence with genomic sequence, allowing for introns.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Matlab toolbox that implements the wavelet-based image fusion technique for orthogonal images, introduced in (Aganj et al, MRM 2012).

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• SciCrunch
• 13 years ago - by Anonymous

Interoperability framework which supports integrative genomics analysis via access to various bioinformatics tools. Rather than performing analyses itself, GenomeSpace acts as a hub for data from supported bioinformatics tools and reformats data and results when necessary.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen