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Software tool to quantitatively measure genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.
Proper citation: BUSCO (RRID:SCR_015008) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for analyzing cross-linking/mass spectrometry datasets using any bifunctional cross-linker. It can be used to identify cross links of peptides – such as DSS, BS3, Disulfides, and zero-length – in complex mixtures.
Proper citation: StavroX (RRID:SCR_014957) Copy
Cross-platform visualization software system for 3D computer graphics, image processing, and data visualization. Various visualization algorithms and advanced modeling techniques are supported within VTK, as well as parallel processing and interoperability with select databases.
Proper citation: VTK (RRID:SCR_015013) Copy
https://www.cpib.ac.uk/tools-resources/software/roottrace/
Software tool which allows the automatic and high throughput measure of root length, as well as extra associated measures such as curvature. The user must supply start points for each root, and exemplar patches of nearby background. The software will then trace the main root to the tip, in every image in a timeseries, and record the results.
Proper citation: RootTrace (RRID:SCR_015585) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 5,2026.ImageJ plugin that performs semiautomated analysis of randomly selected sets of nervous system fibers.
Proper citation: GRatio for ImageJ (RRID:SCR_015580) Copy
Software that analyzes and estimates heritability. LDAK adjusts for linkage disequilibrium (LD) by calculating SNP weightings which downweight the contribution of SNPs in highly tagged regions.
Proper citation: LDAK (RRID:SCR_015504) Copy
https://sourceforge.net/projects/giira/
Gene prediction method that identifies potential coding regions based on the mapping of reads from an RNA-Seq experiment.
Proper citation: GIIRA (RRID:SCR_015507) Copy
http://cerebrovascularportal.org
Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data.
Proper citation: Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) Copy
http://shiny.chemgrid.org/boxplotr/
Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox.
Proper citation: BoxPlotR (RRID:SCR_015629) Copy
https://clinicalstudydatarequest.com/Default.aspx
Consortium of clinical study data providers. Its aim is to help the data sharing community drive scientific progress and improve medical care by facilitating access to patient-level data from clinical studies.
Proper citation: ClinicalStudyDataRequest.com (CSDR) (RRID:SCR_015512) Copy
https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/magicblast/
Software tool for making a BLAST database from various data structures. It maps large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.
Proper citation: MagicBlast (RRID:SCR_015513) Copy
http://mmpc.ucdavis.edu/index.php
Center that provides the scientific community with metabolic and physiologic phenotyping tests, services, and procedures for mouse models of diabetes, diabetic complications, obesity and related disorders in order to advance medical and biological research.
Proper citation: MMPC-University of California Davis (RRID:SCR_015357) Copy
Research center that supports clinical investigation addressing the etiology of nutritionally induced chronic diseases across the entire age span, from gestational and perinatal development through childhood and adolescence. It provides core services to promote the investigations around the theme of molecular mechanisms of nutritional programming induced by environmental factors.
Proper citation: Pennington Biomedical Research Center Nutrition and Obesity Research Center (RRID:SCR_015438) Copy
Research center for obesity investigators which aims to provide researchers with infrastructure, expertise, and training to facilitate improved data integration, analysis and modeling from properly designed basic, clinical, and population-based studies in obesity and metabolism-related diseases.
Proper citation: University of Michigan Nutrition and Obesity Research Center (RRID:SCR_015457) Copy
http://CRAN.R-project.org/package=LMERConvenienceFunctions
Software package that performs backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization.
Proper citation: R package: LMERConvenienceFunctions (RRID:SCR_015658) Copy
https://cran.r-project.org/web/packages/lattice/index.html
Data visualization software inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs as well as most nonstandard requirements.
Proper citation: R package: lattice (RRID:SCR_015662) Copy
http://www.softgenetics.com/GeneMarker.php
Genotype analysis software which enhances the speed, accuracy, and ease of analysis. The software is an alternative to Applied BioSystems Genotyper®, GeneScan®, and other genotype analysis software.
Proper citation: GeneMarker (RRID:SCR_015661) Copy
Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence.
Proper citation: TISSUES (RRID:SCR_015665) Copy
http://csb.pitt.edu/erc_analysis/Methods.php
Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes.
Proper citation: Evolutionary Rate Covariation (RRID:SCR_015669) Copy
http://www.uab.edu/medicine/hrfdcc/
Center that focuses on understanding the causes of Cystic Kidney Disease and other related disorder and the development of new therapeutic strategies.
Proper citation: UAB Hepatorenal Fibrocystic Diseases Core Center (RRID:SCR_015311) Copy
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