Curator Dashboard

Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions.

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• SciCrunch
• 13 years ago - by Anonymous

Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 25,2022. Project (2001-2004) to build and deploy a prototype infrastructure for making scholarly claims about the significance of research documents. "Claims" are made by making connections between ideas. Any claim is open to counterarguments. The connections are grounded in a discourse/argumentation ontology, which makes possible innovative services for navigating, visualizing and analyzing the network as it grows. They have evolved a suite of prototype tools for modelling conceptual networks of ideas and arguments, publishing them for reuse and argumentation, and navigating, searching and filtering this repository as it grows. Some of these are freely available to play with, but WARNING! they are no longer able to support them. The system they have built is called ClaiMaker. Others include ClaimSpotter, ClaiMapper, ClaimFinder, ClaimBlogger and ClaiMaker Microsoft Word plug-in. Additionally, the ScholOnto RDF Schema is available, http://projects.kmi.open.ac.uk/scholonto/resources/Scholonto2.rdfs User Communities: They envisage such a tool as having potential not only in scholarly publishing, but for corporate knowledge analysis, and in education. Complementary work: ScholOnto's focus on net-centric representations of research is complemented by work on augmenting more conventional textual documents, with threaded commentary and debate. An open source web publishing tool is available called D3E (Digital Document Discourse Environment). Many applications are illustrated on the site, including the award-winning Journal of Interactive Media in Education.We are no longer able to support tools, so are not able to assist if you have problems or lose data.

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• SciCrunch
• 14 years ago - by Anonymous

Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.

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• SciCrunch
• 12 years ago - by Anonymous

Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.

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• SciCrunch
• 12 years ago - by Anonymous

Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.

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• SciCrunch
• 16 years ago - by Anonymous

A software package to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them. It establishes common bins across tubes in terms of the common markers, then determines expression within each tube for each bin in terms of the tube-specific markers.

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• SciCrunch
• 12 years ago - by Anonymous

A command line software utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.

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• SciCrunch
• 12 years ago - by Anonymous

Software for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing.

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• SciCrunch
• 13 years ago - by Anonymous

A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.

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• SciCrunch
• 13 years ago - by Anonymous

A software tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly.

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• SciCrunch
• 11 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations.

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• SciCrunch
• 12 years ago - by Anonymous

Software application that uses change point model for detecting 3-prime UTR changes by RNA-Seq.

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• SciCrunch
• 11 years ago - by Anonymous

Software providing an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs.

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• SciCrunch
• 11 years ago - by Anonymous

Software visualization tool based on the VTK library. Its main feature is to measure and display surface-to-surface distance between two triangle meshes using user-specified uniform sampling. Offers all the basic tools to visualize meshes such as color, opacity, smoothing, down sampling or type of representation.

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• SciCrunch
• 13 years ago - by Anonymous

A software tool that allows multi-locus and multi-level association analysis of genotypic and phenotypic data.

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• SciCrunch
• 11 years ago - by Anonymous