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on page 1 showing 20 out of 98 results from 1 sources

    AnnTools

Cite this (AnnTools, RRID:SCR_005170)

URL: http://anntools.sourceforge.net/

Resource Type: Resource, software resource

Software tool for annotating single nucleotide substitutions (SNP/SNV), small insertions/deletions (indels), and copy number variations (CNV) calls generated from sequencing and microarray data. Only human genome build 37/hg19 can be annotated at this time.

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Cite this (ANTS - Advanced Normalization ToolS, RRID:SCR_004757)

URL: http://www.picsl.upenn.edu/ANTS/

Resource Type: Resource, segmentation software, image analysis software, data processing software, software application, software resource, registration software

Software package designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic*, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). *Diffeomorphism: a differentiable map with differentiable inverse. In general, these maps are generated by integrating a time-dependent velocity field. ANTS Applications: * Gray matter morphometry based on the jacobian and/or cortical thickness. * Group and single-subject optimal templates. * Multivariate DT + T1 brain templates and group studies. * Longitudinal brain mapping -- special similarity metric options. * Neonatal and pediatric brain segmentation. * Pediatric brain mapping. * T1 brain mapping guided by tractography and connectivity. * Diffusion tensor registration based on scalar or connectivity data. * Brain mapping in the presence of lesions. * Lung and pulmonary tree registration. * User-guided hippocampus labeling, also of sub-fields. * Group studies and statistical analysis of cortical thickness, white matter volume, diffusion tensor-derived metrics such as fractional anisotropy and mean diffusion.

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    ANTsR

Cite this (ANTsR, RRID:SCR_008891)

URL: http://www.nitrc.org/projects/antsr

Resource Type: Resource, software resource

An R extension to ANTs that performs multivariate statistical parametric mapping of DTI, T1 and other datatypes for the purpose of both performing clinical studies and for tracking the performance of ANTs (and other) image processing methodologies. ANTsR depends upon the R statistical language, bash scripts and the ANTs toolkit. Some branches of ANTsR will also depend upon pipedream and specific datasets. Some of these datasets will be open access and, in that case, ANTsR will provide a 100% reproducible neuroimaging study on that data.

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    ARCTIC

Cite this (ARCTIC, RRID:SCR_005989)

URL: http://www.nitrc.org/projects/arctic

Resource Type: Resource, software resource, software application, workflow software, data processing software, image analysis software

An end-to-end application allowing individual regional analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line. * Operating System: MacOS, Linux * Programming Language: C++ * Supported Data Format: ANALYZE, Nrrd, Other Format * build requires: Insight Toolkit

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Cite this (arrayMagic, RRID:SCR_010933)

URL: http://bioconductor.org/packages/2.1/bioc/html/arrayMagic.html

Resource Type: Resource, software resource

Software providing a collection of utilities for quality control and processing of two-colour cDNA microarray data

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Cite this (AStalavista, RRID:SCR_001815)

URL: http://sammeth.net/confluence/display/ASTA/2+-+Download

Resource Type: Resource, software resource, analysis service resource, data analysis service, service resource, production service resource

Tool that extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, it detects the variations in their splicing structure and identifies all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. It provides a visual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase, etc.

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Cite this (Atrophy Simulation Package, RRID:SCR_006046)

URL: http://www.rad.upenn.edu/sbia/

Resource Type: Resource, software resource, software application, simulation software

Software package used to simulate brain images with local growth / atrophy within a prescribed spherical region. Specifically, given an input image and its segmented image, the location of the center of the spherical region, and the radius of that sphere, it simulates new images that have tissue growth or shrinkage within that pre-specified brain region according to given rates (atrophy for rates less than one and growth for rates greater than one). The algorithm uses an iterative procedure that tries to achieve the given level of volumetric change for brain tissues within the region, by seeking a smooth deformation field, whose Jacobian determinants match the prescribed volume change rate within the region. Note that in the current software, the simulation of growth or atrophy for brain tissue requires that the input spherical region has to cover some CSF or background regions.

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    AutoSeg

Cite this (AutoSeg, RRID:SCR_009438)

URL: http://www.nitrc.org/projects/autoseg/

Resource Type: Resource, software resource, image analysis software, data processing software, software application

A novel C++ based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation. AutoSeg is designed for use with human and non-human primate pediatric, adolescent and adult data. AutoSeg uses a BatchMake pipeline script that includes the main steps of the framework entailing N4 bias field correction, rigid registration to a common coordinate image, tissue segmentation, skull-stripping, intensity rescaling, atlas-based registration, subcortical segmentation and lobar parcellation, regional cortical thickness and intensity statistics. AutoSeg allows efficient batch processing and grid computing to process large datasets and provides quality control visualizations via Slicer3 MRML scenes.

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    BAIT

Cite this (BAIT, RRID:SCR_000511)

URL: http://sourceforge.net/projects/bait/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

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Cite this (Batch Oligo Selection Script, RRID:SCR_002808)

URL: http://sourceforge.net/projects/b-o-s-s/

Resource Type: Resource, software resource

A batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps.

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    BrainCSI

Cite this (BrainCSI, RRID:SCR_013244)

URL: http://www.softpedia.com/get/Science-CAD/BrainCSI.shtml

Resource Type: Resource, software resource, image analysis software, data processing software, software application

A tool for analysis of Magnetic Resonance Spectroscopy (MRS) data by registering it to anatomical images. BrainCSI imports LCModel results to calculate absolute metabolite concentrations using tissue water. Corrections to LCModel metabolite concentrations for partial volume of tissues are accomplished by tissue classification of the anatomical images.

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Cite this (BRAINSCortex, RRID:SCR_001082)

URL: https://github.com/BRAINSia/BRAINSTools

Resource Type: Resource, software resource, software toolkit, software application

A suite of tools to generate the cortical surface of the brain. The surface is generated in the middle of grey matter and can be used to measure surface features including cortical depth and curvature.

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Cite this (BRAINSCut, RRID:SCR_000861)

URL: https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSCut

Resource Type: Resource, segmentation software, image analysis software, data processing software, software resource, software application

A software package for segmentation of structures using automated neual networks. This is the reference implementation using NAMIC software development best practices and the Insight Toolkit of the paper Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures. (PMID: 17904870). The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.

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Cite this (BRAINSFit, RRID:SCR_002340)

URL: https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSFit

Resource Type: Resource, software resource, image analysis software, registration software, data processing software, software application

A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3

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Cite this (BRAINSMush, RRID:SCR_009485)

URL: https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSMush

Resource Type: Resource, segmentation software, image analysis software, data processing software, software resource, software application

Tool to generate brain volume mask from input of T1 and T2-weighted images alongside a region of interest brain mask. This volume mask omits dura, skull, eyes, etc. The program is built upon ITK and uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.

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Cite this (BRAINSSurfaceStats, RRID:SCR_002582)

URL: http://www.nitrc.org/projects/surfacestat/

Resource Type: Resource, software resource, software application, data processing software

Software tool for performing a per vertex statistical analysis across a population. The underlying statistical framework uses the R language.

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    BSMac

Cite this (BSMac, RRID:SCR_009531)

URL: http://web1.sph.emory.edu/bios/CBIS/download_page.php

Resource Type: Resource, software resource, software toolkit, software application, data processing software, image analysis software

A statistical and graphical visualization MATLAB toolbox for the analysis of fMRI data, called the Bayesian Spatial Model for activation and connectivity (BSMac). BSMac simultaneously performs whole-brain activation analyses at the voxel and region of interest levels as well as task-related functional connectivity (FC) analyses using a flexible Bayesian modeling framework (Bowman et al., 2008). BSMac allows for inputting data in either Analyze or Nifti file formats. The user provides information pertaining to subgroup memberships, scanning sessions, and experimental tasks (stimuli), from which the design matrix is constructed. BSMac then performs parameter estimation based on MCMC methods and generates plots for activation and FC, such as interactive 2D maps of voxel and region-level task-related changes in neural activity and animated 3D graphics of the FC results.

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    caGWAS

Cite this (caGWAS, RRID:SCR_009617)

URL: https://wiki.nci.nih.gov/display/caGWAS/caGWAS

Resource Type: Resource, software resource

Too that allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response or other clinical outcomes. SNP array technologies make it possible to genotype hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously, enabling whole genome association studies. Within the Clinical Genomic Object Model (CGOM), the caIntegrator team created a domain model for Whole Genome Association Study Analysis. CGOM-caGWAS is a A semantically annotated domain model that captures associations between Study, Study Participant, Disease, SNP Association Analysis, SNP Population Frequency and SNP annotations. caGWAS APIs and web portal provide: * a semantically annotated domain model, database schema with sample data, seasoned middleware, APIs, and web portal for GWAS data; * platform and disease agnostic CGOM-caGWAS model and associated APIs; * the opportunity for developers to customize the look and feel of their GWAS portal; * a foundation of open source technologies; * a well-tested and performance-enhanced platform, as the same software is being used to house the CGEMS data portal; * accelerated analysis of results from various biomedical studies; and * a single application through which researchers and bioinformaticians can access and analyze clinical and experimental data from a variety of data types, as caGWAS objects are part of the CGOM, which includes microarray, genomic, immunohistochemistry, imaging, and clinical data.

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Cite this (CCDB Image Converter, RRID:SCR_007005)

URL: http://openccdb-dev-web.crbs.ucsd.edu/software/index.shtm

Resource Type: Resource, software resource

A command line program in Unix to convert images to a variety of formats (PNG, TIFF, JPEG, PPM..etc). It is uniquely different from other programs such as Adobe Photoshop or ImageMagick because it is designed for dealing with the high-resolution images with file sizes of several gigabytes. Image Converter does not require any additional RAM or virtual memory to run. Also, run-time is relatively fast for high resolution data.

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Cite this (CCSeg - Corpus Callosum Segmentation, RRID:SCR_009453)

URL: http://www.nitrc.org/projects/ccseg/

Resource Type: Resource, segmentation software, image analysis software, data processing software, software resource, software application

An open-source C++-based application that allows automatic as well as user-interactive segmentation of the Corpus Callosum. Via a Qt-based graphical user interface, CCSeg also performs semi-automatic segmentation.

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