Curator Dashboard

Software Python package for detection, alignment and reporting of recombination events in Next-Generation Sequencing data. Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 12 years ago - by Anonymous

Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions.

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• SciCrunch
• 12 years ago - by Anonymous

Software that identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as Rejected Substitutions. Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element. GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns. A false-positive rate (which is user-settable) is calculated using "shuffled" alignments in which the order of columns is randomized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 12 years ago - by Anonymous

A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. Database of information about brain region circuitry, it collates data from the literature on tract tracing studies and provides tools for analysis and visualization of connectivity between brain regions., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 15 years ago - by Anonymous

Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

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• SciCrunch
• 13 years ago - by Anonymous

Multi-purpose SNV calling software enhanced by probabilistic integration of quality scores.

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• SciCrunch
• 12 years ago - by Anonymous

Software for reliable Identification of Genomic Variants Using RNA-seq Data.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome.

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• SciCrunch
• 13 years ago - by Anonymous

Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.

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• SciCrunch
• 13 years ago - by Anonymous

Interactive demonstrations of sensory perception phenomena from Dale Purves' website. You may read the empirical explanations and download high resolution images.

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• SciCrunch
• 15 years ago - by Anonymous

Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. Software tool for estimating Species Richness Using 16S rRNA Pyrosequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 12 years ago - by Anonymous

The Alzheimer's Disease Research Center at Emery University maintains an active brain bank to facilitate the acquisition, storage, handling and distribution of well-characterized autopsy brain tissue and other materials to investigators. It contains frozen tissue and brain specimens, formalin fixed tissue, paraformaldehyde fixed tissue, and cryopreserved tissue. The ADRC also has access to tissues and samples related to other neurodegenerative diseases. It contains plasma samples, serum samples, lymphoblast cell lines, and cerebrospinal fluid.

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• SciCrunch
• 15 years ago - by Anonymous

NDRI is a Not-For-Profit (501c3) Corporation dedicated to providing the highest quality human biomaterials for research. NDRI makes it easy for researchers to get the human tissues and organs they need, prepared, preserved and shipped precisely according to their specific scientific protocols, as quickly as possible, and in the largest available quantities. NDRI provides researchers with protocol specific human neurological tissues such as brain stem, spinal cord, and basal ganglia, among others. In addition to control specimens, NDRI recovers tissues from donors with a variety of diseases, including Down syndrome, Parkinsons disease, Alzheimers disease, schizophrenia, and dementia. Through the NDRI 24/7 referral and procurement system, research consented biospecimens can be provided from low post mortem interval donors preserved at 4ºC, frozen or snap frozen, fixed, paraffin embedded, or as unstained slides.

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• SciCrunch
• 15 years ago - by Anonymous

A non-profit organization that facilitates the donation of tissues. It supports healthcare agencies, coroners, medical examiners and funeral professionals through donations and training, as well as partnering with organizations that utilize tissue in medical care and research.

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• SciCrunch
• 15 years ago - by Anonymous

A nonprofit organ procurement agency based in Iowa. The organization facilitates both organ and tissue recovery in cooperation with local hospitals. The network also works to support public education, hospital development and family support services.

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• SciCrunch
• 15 years ago - by Anonymous

A neuroscience PhD program based at Indiana University that focuses on technical skills and the conceptual framework needed to puruse a career of research and/or teaching in neuroscience. Faculty of the neuroscience department fall into one of four areas of research: Molecular and Cellular Neuroscience, Behavioral Neuroscience, Cognitive and Computational Neuroscience and Clinical and Translational Neuroscience.

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• SciCrunch
• 16 years ago - by Anonymous