Curator Dashboard

Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects.

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• SciCrunch
• 9 years ago - submitted by Fernando Meyer

Rabbit monoclonal antibody raised against the -Val-Ile-Pro-Arg-Ser in the C-terminus. Edwards et al. Biochem Pharmacol. 1998 Aug 1;56(3):377-87. PubMed PMID: 9744576

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• SciCrunch
• 9 years ago - submitted by Jonathan Peterson

Software for an integrated network combining multiple biological network database sources into a single human protein interactome. The software package contains gene interaction pairs corresponding to the unified global network.

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• RRID-Legacy
• 9 years ago - by Anonymous

Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium.

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• RRID-Legacy
• 9 years ago - by Anonymous

Database for investigating and visualizing protein-protein interactions. It aims to maintain coverage, quality, convenience, and transparency in the field of PPI research.

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• RRID-Legacy
• 9 years ago - by Anonymous

Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes.

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• RRID-Legacy
• 9 years ago - by Anonymous

Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations.

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• RRID-Legacy
• 9 years ago - by Anonymous

Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection.

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• RRID-Legacy
• 9 years ago - by Anonymous

Hardware that is used to test and assess pain and inflammation of the hind limbs on mice and rats. Dynamic weight bearing enables the test to be implemented on both limbs, while inflicting less stress on the subject animal.

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• RRID-Legacy
• 9 years ago - by Anonymous

Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience.

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• RRID-Legacy
• 9 years ago - by Anonymous

Software for a Python feature selection repository that contains a variety of feature selection algorithms, including traditional feature selection algorithms and some structural and streaming feature selection algorithms. It serves as a platform for facilitating feature selection application, research and comparative study.

• RRID-Legacy
• 9 years ago - submitted by David Kennedy

Software for a bioinformatics pipeline that generates a superTranscriptome from popular fusion finder outputs (JAFFA, tophatFusion, SOAP, deFUSE, Pizzly, etc). They can be then be either viewed in genome viewers such as IGV or through the included plotting feature developed with GViz.

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• SciCrunch
• 9 years ago - submitted by Breon Schmidt

Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information.

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• SciCrunch
• 9 years ago - submitted by Christoph Ziegenhain

Software application for data manipulation, calculation and graphical display. Used for statistical computing and graphics and provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, …) and graphical techniques, and is highly extensible. R provides an Open Source route to participation in statistical methodology. It compiles and runs on a wide variety of UNIX platforms and similar systems (including FreeBSD and Linux), Windows and MacOS.

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• SciCrunch
• 9 years ago - submitted by Edyta Vieth

Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.

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• SciCrunch
• 9 years ago - submitted by Edyta Vieth

long read genome assembler based on hinging HINGE is a genome assembler that seeks to achieve optimal repeat resolution by distinguishing repeats that can be resolved given the data from those that cannot. This is accomplished by adding “hinges” to reads for constructing an overlap graph where only unresolvable repeats are merged. As a result, HINGE combines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de Bruijn graph assemblers.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Used for sequence-based protein function and structure prediction what depends on sequence-search sensitivity and accuracy of the resulting sequence alignments.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman