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http://sourceforge.net/projects/samzip/

An encoding and decoding tool for Sequence Alignment/Map (SAM) files.

Proper citation: SAMZIP (RRID:SCR_012980) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://ccb.jhu.edu/software/tophat/index.shtml

Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.

Proper citation: TopHat (RRID:SCR_013035) Copy   

•   Source: SciCrunch Registry

http://www.viprbrc.org/brc/home.do?decorator=vipr

Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research.

Proper citation: Virus Pathogen Resource (ViPR) (RRID:SCR_012983) Copy   

•   Source: SciCrunch Registry

http://sammate.sourceforge.net/

An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

Proper citation: SAMMate (RRID:SCR_013037) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/flexbar/

Flexible barcode and adapter removal for sequencing platforms.

Proper citation: Flexbar (RRID:SCR_013001) Copy   

•   Source: SciCrunch Registry

http://www.cochrane.org/reviews/clibintro.htm

Contains data to inform healthcare decision-making from Cochrane and other systematic reviews, clinical trials, and more. Cochrane reviews bring you the combined results of the worlds best medical research studies, and are recognized as the gold standard in evidence-based health care. Consists of a regularly updated collection of evidence-based medicine databases, including The Cochrane Database of Systematic Reviews. This database includes systematic reviews of healthcare interventions that are produced and disseminated by The Cochrane Collaboration. It is published on a monthly basis and made available both on CD-ROM and the Internet. The review abstracts are available to browse and search free of charge on this website. The Cochrane Library Users'' Group (CLUG) provides a forum for discussion of usability, readability, searchability, and formatting issues related to the use of The Cochrane Library. The Cochrane Collaboration is an international not-for-profit and independent organization, dedicated to making up-to-date, accurate information about the effects of healthcare readily available worldwide. Funded by John Wiley and Sons Limited. The individual entities of The Cochrane Collaboration are funded by a large variety of governmental, institutional and private funding sources, and are bound by organisation-wide policy limiting uses of funds from corporate sponsors.

Proper citation: Cochrane Library (RRID:SCR_013000) Copy   

•   Source: SciCrunch Registry

http://rnai.dkfz.de

GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome

Proper citation: GenomeRNAi (RRID:SCR_013088) Copy   

•   Source: SciCrunch Registry

http://www.nccn.org/

A not-for-profit alliance of 23 cancer centers devoted to patient care, research, and education, is dedicated to improving the quality, effectiveness, and efficiency of cancer care so that patients can live better lives. Through the leadership and expertise of clinical professionals at NCCN Member Institutions, NCCN develops resources that present valuable information to the numerous stakeholders in the health care delivery system. As the arbiter of cancer care, NCCN promotes the importance of continuous quality improvement and recognizes the significance of creating clinical practice guidelines appropriate for use by patients, clinicians, and other health care decision-makers.

Proper citation: NCCN (RRID:SCR_012959) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/shrec-ec/

A bioinformatics tool for error correction of HTS read data.

Proper citation: SHREC (RRID:SCR_013009) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hictools/

This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond.

Proper citation: hiCtools (RRID:SCR_013010) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/locas/

A software to assemble short reads of next generation sequencing technologies at low coverage.

Proper citation: LOCAS (RRID:SCR_013064) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vdjfasta/?source=navbar

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires.

Proper citation: VDJFasta (RRID:SCR_013069) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vcake/

A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error.

Proper citation: VCAKE (RRID:SCR_013060) Copy   

•   Source: SciCrunch Registry

http://derisilab.ucsf.edu/software/price/index.html

Software for a de novo genome assembler implemented in C++.

Proper citation: PRICE (RRID:SCR_013063) Copy   

•   Source: SciCrunch Registry

http://www.nhlbi.nih.gov/about/dld/

Supports research on the causes, diagnosis, prevention, and treatment of lung diseases and sleep disorders. Research is funded through investigator-initiated and Institute-initiated grant programs and through contract programs in areas including asthma, bronchopulmonary dysplasia, chronic obstructive pulmonary disease, cystic fibrosis, respiratory neurobiology, sleep-disordered breathing, critical care and acute lung injury, developmental biology and pediatric pulmonary diseases, immunologic and fibrotic pulmonary disease, rare lung disorders, pulmonary vascular disease, and pulmonary complications of AIDS and tuberculosis. The Division is responsible for monitoring the latest research developments in the extramural scientific community as well as identifying research gaps and needs, obtaining advice from experts in the field, and implementing programs to address new opportunities. The DLD has three branches, the Airway Biology and Disease Branch, the Lung Biology and Disease Branch, and the National Center on Sleep Disorders Research.

Proper citation: NHLBI Division of Lung Diseases (RRID:SCR_013074) Copy   

•   Source: SciCrunch Registry

http://www.nichd.nih.gov/research/supported/pages/tbi.aspx

The National Center for Medical Rehabilitation Research (NCMRR) established a multi-center network of sites that are working together to design clinical intervention protocols and measures of outcome for TBI. Through rigorous patient evaluation, using common protocols and interventions designed for multiple points of care����??including the accident scene, emergency room, intensive care unit, rehabilitation and long-term follow-up����??the NCMRR TBI Clinical Trials Network can study the required numbers of patients to provide answers more rapidly than individual centers acting alone. This interdisciplinary research Network is designed to evaluate the relationship among acute care practice, rehabilitation strategies, and the long-term functional outcome of TBI patients����??that is, to identify which intervention variables result in improvements in long-term outcomes. Taking advantage of the network model structure has allowed TBI research to progress toward a number of clinical research goals. Specifically, the NCMRR wants to highlight two major achievements to date. First, the TBI Network created a profile of its typical patient to determine the number of patients with different clinical features who might be eligible for future studies and to help estimate recruitment times necessary. Second, Network researchers are developing clinical treatment guidelines and procedures for all points in the continuum of care, including TBI Clinical Trials Network Guidelines for surgical care, systems-based protocol for severe and moderate TBI patients, deep-vein thrombosis prophylaxis procedures, and rehabilitation guidelines for physical therapy, speech-language pathology, occupational therapy, and neuropsychology.

Proper citation: Traumatic Brain Injury Clinical Trials Network (RRID:SCR_013165) Copy   

•   Source: SciCrunch Registry

https://confluence.crbs.ucsd.edu/display/NIF/OntoQuestMain

An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework.

Proper citation: OntoQuest (RRID:SCR_013281) Copy   

•   Source: SciCrunch Registry

http://www.mi.med.osaka-u.ac.jp/gpetview/gpetview.html

GpetView is light-weight image viewer based on Gtk+ library. The supported image format is ANALYZE(TM) format (Mayo Foundation ). GpetView can run on Unix-systems, such as Linux, Solaris, IRIX, Mac OS-X etc. From Version 2.0, GpetView can also run on Win32 system, if you have installed Glib and Gtk+(2.x). Glib andGtk+ can be found at http://www.gtk.org. For Windows users, you can find Gtk+ libraries at http://gladewin32.sourceforge.net/modules/news/ GpetView has the following features: * very light-weight * view images as transverse, coronal, or sagittal * change color-map (support Analyze lkup file) * zoom images * ROI (Region-Of-Interest) with shapes of circle, ellipse, rectangle, polygon and automatic edge detection * Image histogram and profile Sponsors: This resource is supported by Osaka University. Keywords: Image, Viewer, Software, Transverse, Coronal, Sagittal, Map, Histogram,

Proper citation: Gtk-based Analyze Image Viewer (RRID:SCR_013282) Copy   

•   Source: SciCrunch Registry

http://www.aans.org/

The American Association of Neurological Surgeons is dedicated to advancing the specialty of neurological surgery and serving as the spokes organization for all practitioners of the specialty of neurosurgery, in order to provide the highest quality of care to our patients. :Founded in 1931 as the Harvey Cushing Society, the American Association of Neurological Surgeons (AANS) is a scientific and educational association with over 7,400 members worldwide. The AANS is dedicated to advancing the specialty of neurological surgery in order to provide the highest quality of neurosurgical care to the public. All Active members of the AANS are board certified by the American Board of Neurological Surgery, the Royal College of Physicians and Surgeons of Canada, or the Mexican Council of Neurological Surgery, A.C. Neurosurgery is the medical specialty concerned with the prevention, diagnosis, treatment and rehabilitation of disorders that affect the spinal column, spinal cord, brain, nervous system and peripheral nerves. For more information on what neurosurgeons do, visit our public pages at : :www.NeurosurgeryToday.org : : :. Visitors to our Web site can find Member Counts under membership including demographic details.

Proper citation: American Association of Neurological Surgeons (RRID:SCR_013209) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages//2.10/bioc/html/HiTC.html

Software package to explore high-throughput ''C'' data such as 5C or Hi-C.

Proper citation: HiTC (RRID:SCR_013175) Copy   

•   Source: SciCrunch Registry