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http://paleogenomics.irmacs.sfu.ca/FPSAC/
Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.
Proper citation: FPSAC (RRID:SCR_000555) Copy
http://bbc.mdc-berlin.de/software
Multi-purpose SNV calling software enhanced by probabilistic integration of quality scores.
Proper citation: ACCUSA2 (RRID:SCR_000558) Copy
Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).
Proper citation: RStudio (RRID:SCR_000432) Copy
https://code.google.com/p/dysc/
Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy.
Proper citation: DySC (RRID:SCR_000553) Copy
https://nei.nih.gov/health/clinicalstudies/
An archived portal of clinical studies, both ongoing and completed, that have been conducted and supported by the National Eye Institute (NEI) since 1970. The portal covers corneal diseases, glaucoma, epidemiology, lens and cataract, retinal diseases, strabismus, amblyopia and visual processing.
Proper citation: NEI Clinical Studies (RRID:SCR_000546) Copy
https://sourceforge.net/projects/popbam/
A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.
Proper citation: POPBAM (RRID:SCR_000464) Copy
http://drfast.sourceforge.net/
A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.
Proper citation: drFAST (RRID:SCR_000586) Copy
http://genome.crg.es/software/gfftools/GFF2PS.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.
Proper citation: Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) Copy
http://bioinfo2.ugr.es/NGSmethPipe/
A software tool which generates high-quality methylation maps.
Proper citation: NGSmethPipe (RRID:SCR_000583) Copy
https://cran.r-project.org/src/contrib/Archive/sybil/
A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.
Proper citation: sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) Copy
https://github.com/holtjma/msbwt
A software package for creating, merging, and querying multi-string BWTs.
Proper citation: msbwt (RRID:SCR_000458) Copy
http://www.stanford.edu/~cpatton/maxc.html
A series of programs for determining the free metal concentration in the presence of chelators or total metal given a desired free concentration.
Proper citation: MAXCHELATOR (RRID:SCR_000459) Copy
http://bioconductor.org/packages/release/bioc/html/Rdisop.html
Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.
Proper citation: Rdisop (RRID:SCR_000453) Copy
http://bsec.ornl.gov/AdaptiveCrawler.shtml
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. A web crawler that can intelligently acquire social media content on the Internet to meet the specific online data source acquisition needs of cancer researchers.
Proper citation: AdaptiveCrawler (RRID:SCR_000573) Copy
The mission of the National Spasmodic Dysphonia Association is to advance medical research into the causes of and treatments for spasmodic dysphonia, promote physician and public awareness of the disorder, and provide support to those affected by spasmodic dysphonia.
Proper citation: National Spasmodic Dysphonia Association (RRID:SCR_000447) Copy
https://resource.loni.usc.edu/resources/atlases/
Probabilistic reference system for human brain, including tools to establish this reference system for structural and functional anatomy on both macroscopic (in vivo) and microscopic (post mortem) levels. Project has expanded neuroinformatics tools for data sharing and created Conforming Site System that allows laboratories worldwide to contribute data to evolving atlas. Through implementation of ICBM data sharing policy space, they are fostering data exchange while still providing for scientific credit assignment and subject confidentiality.ICBM atlas collection consists of ICBM Template, tool developed to provide reference that includes both set of coordinates and associated anatomical labels; the ICBM 452 T1 atlas, average of T1-weighted MRIs of normal young adult brains, ICBM probabilistic atlases, and Cytoarchitectonic Atlas. ICBM Subject Database is web-based database infrastructure that simplifies image dataset collection, organization and dissemination. Authorized users may view representations of data and form collections of datasets that can be downloaded or fed directly into Pipeline environment for distributed processing and analysis.
Proper citation: International Consortium for Brain Mapping (RRID:SCR_000445) Copy
Software automated coordinate based system to retrieve brain labels from the 1988 Talairach Atlas. Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach Atlas.
Proper citation: Talairach Daemon (RRID:SCR_000448) Copy
https://github.com/PacificBiosciences/stsPlots
Software to plot primary analysis quality control metrics to assess potential SMRTcell loading problems.
Proper citation: stsPlots (RRID:SCR_000449) Copy
A division of the Stanford University Libraries, which produces the online versions of journals and other scholarly content.
Proper citation: HighWire Press (RRID:SCR_000761) Copy
http://w3.cns.org/university/webinar/index2.asp
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. A series of of webinars offered directly to users' computers. The webinars are offered in a variety of subjects, including neurotrauma, spine, tumor and vascular. Each webinars costs $35 US and offers CME credit.
Proper citation: University of Neurosurgery Webinar Series (RRID:SCR_000639) Copy
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