Curator Dashboard

Software functions for data analysis and graphical displays for developmental microarray time course data.

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• SciCrunch
• 12 years ago - by Anonymous

A free bioinformatics software tool to help identify fusion transcripts from paired-end transcriptome sequencing data. The source codes of SnowShoes-FTD are provided in two formats: one configured to run on the Sun Grid Engine for parallelization with shorter run time, and the other formatted to run on a single LINUX node.

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• SciCrunch
• 12 years ago - by Anonymous

Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.

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• SciCrunch
• 12 years ago - by Anonymous

Software package to annotate variants, compute amino acid coding changes, and predict coding outcomes.

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• SciCrunch
• 12 years ago - by Anonymous

Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.

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• SciCrunch
• 12 years ago - by Anonymous

Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data.

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• SciCrunch
• 12 years ago - by Anonymous

A Brazilian laboratory dedicated to conducting research, developing and training of human resources for scientific computing. There is a special emphasis on the construction and application of mathematical and computational models for solving scientific and technological problems. They also provide a computing environment for high-performance processing in order to conduct research. This organization's website is in Spanish.

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• SciCrunch
• 12 years ago - submitted by

A supplier of cancer and infectious disease diagnostic reagents. The company also provides services such as tissue-based and molecular diagnostics to their partners to accelerate their in vitro diagnostic device (IVD) product development and commercialization.

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• SciCrunch
• 13 years ago - by Anonymous

An antibody supplier for the purposes of life science and biomedical research. This company has a wide variety of immunological reagents that focus on areas of research such as cancer, cell biology, epigenetics, immunology and infectious diseases.

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• SciCrunch
• 13 years ago - by Anonymous

An open-source C++ software library of classes for the design and analysis of primers suitable for a wide range of PCR applications.

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• SciCrunch
• 11 years ago - by Anonymous

Image registration toolkit for research purposes.Medical Image Registration ToolKit , the successor of the IRTK, contains common CMake build configuration files, core libraries, and basic command-line tools.

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• SciCrunch
• 12 years ago - by Anonymous

Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).

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• SciCrunch
• 12 years ago - by Anonymous

A comprehensive software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform. The MPScope package features the acquisition software MPScan, the analysis program MPView and several software utilities.

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• SciCrunch
• 12 years ago - by Anonymous

The NIH formally established the Division of Program Coordination, Planning, and Strategic Initiatives (DPCPSI) as part of implementing the requirements of the NIH Reform Act of 2006. DPCPSI directs a number of activities, such as: identifying emerging scientific opportunities, rising public health challenges, or scientific knowledge gaps that merit further research; assisting the NIH in addressing areas of emerging scientific opportunities and public health challenges effectively; and planning, supporting, and providing technical assistance in the development of program evaluations. The DPCPSI also coordinates research and activities related to research on AIDS, behavioral and social sciences, womens health, disease prevention, dietary supplements, and research infrastructure.

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• SciCrunch
• 16 years ago - by Anonymous

A department within Colorado College that is dedicated to providing academic programs for undergraduate education. Students are educated in a variety of research techniques, statistics and design experiments.

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• SciCrunch
• 16 years ago - by Anonymous

A homology search software tool for huge short reads generated by next-generation sequencers. It can detect remote homologs like BLAST and is about 40 times more efficient than BLAST by using a GPU-computing technique.

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• SciCrunch
• 11 years ago - by Anonymous

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
• 12 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
• 12 years ago - by Anonymous

Software used to detect gene fusions from paired-end RNA-Seq data.

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• SciCrunch
• 12 years ago - by Anonymous

A transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions.

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• SciCrunch
• 12 years ago - by Anonymous