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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   

•   Source: SciCrunch Registry
  

https://github.com/JiangYuLab/CNVcaller

Software for detecting the integrated copy number variation regions (CNVRs) using population sequencing data. The high-confidence CNVRs are discovered and refined by both individual and population criteria, and the result is a VCF format genotype file which can be used in GWAS/QLT research.

Proper citation: CNVcaller (RRID:SCR_015752) Copy   

•   Source: SciCrunch Registry
  

http://www.einstein.yu.edu/centers/liver-research/

Center that conducts scientific investigation to understand fundamental mechanisms of normal liver function, alterations in these functions resulting from metabolic disorders, genetic diseases, acute and chronic liver injury, hepatitis virus infection, hepatic fibrosis and liver cancer, and ways to overcome these abnormalities through methods of genetic engineering, gene therapy and liver cell transplantation.

Proper citation: Marion Bessin Liver Research Center (RRID:SCR_015190) Copy   

•   Source: SciCrunch Registry
  

http://floresta.eead.csic.es/primers4clades

Web application for the design of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic lineages. It implements an extended CODEHOP strategy and evaluates thermodynamic properties of the oligonucleotide pairs.

Proper citation: primers4clades (RRID:SCR_015714) Copy   

•   Source: SciCrunch Registry
  

https://www.uab.edu/medicine/obriencenter/

Research center for kidney research, specifically acute kidney injury. It supports shared core facilities, encourages collaboration between investigators from different backgrounds and disciplines whose shared interest is in kidney research, and provides intellectual resources and infrastructure.

Proper citation: UAB-UCSD Core Center for Acute Kidney Injury Research (RRID:SCR_015282) Copy   

•   Source: SciCrunch Registry
  

http://www.mightexsystems.com/family_info.php?cPath=245_347_346&categories_id=346

Software used in tandem with the Polygon 400 from Mightex systems to define areas of illumination, control light intensity and duration, and calibrate the device.

Proper citation: Dynamic Spatial Illuminator Software (RRID:SCR_015725) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/bioc/html/oligo.html

Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Proper citation: oligo (RRID:SCR_015729) Copy   

•   Source: SciCrunch Registry
  

https://github.com/BGI-SZ/BSVF

Software code for bisulfite sequencing virus integration. This finder is for directional libraries only and does not support PBAT and indirectional libraries.

Proper citation: BSVF (RRID:SCR_015727) Copy   

•   Source: SciCrunch Registry
  

http://chicagodiabetesresearch.org

Center to improve the lives of people with diabetes and people at risk for diabetes through prevention, improved diabetes care, and community empowerment.

Proper citation: Chicago Center for Diabetes Translation Research (RRID:SCR_015179) Copy   

•   Source: SciCrunch Registry
  

https://www.med.upenn.edu/idom/

NIDDK center that serves diabetes-oriented investigators from University of Pennsylvania as well as additional institutions from the mid-Atlantic region. The Penn DRC represents many basic science and clinical departments at Penn and the other institutions, and supports research in diabetes and obesity via Scientific Cores, a Pilot and Feasibility Grant Program, and a series of seminars, retreats, and other academic enrichment activities.

Proper citation: University of Pennsylvania Diabetes Research Center (RRID:SCR_015732) Copy   

•   Source: SciCrunch Registry
  

https://trendscenter.org/software/

Software toolbox which finds and displays temporal relations amongst components. This can help determine causal relations in the brain.

Proper citation: Functional Network Connectivity (FNC) (RRID:SCR_015731) Copy   

•   Source: SciCrunch Registry
  

http://www.einstein.yu.edu/centers/diabetes-translational-research/

Center designed to increase collaboration and enhance communication among diabetes researchers from multiple institutions and diverse disciplines

Proper citation: New York Regional Center for Diabetes Translation Research (RRID:SCR_015174) Copy   

•   Source: SciCrunch Registry
  

http://www.utsouthwestern.edu/research/core-facilities/obrien-kidney/

Center whose goal is to generate new animal models to study the pathogenesis and treatment of human kidney diseases and their cardiovascular complications, accelerate the clinical application of discoveries made in renal basic science laboratories, and provide investigators with specialized tools and expertise to study kidney development, physiology, and pathophysiology.

Proper citation: George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center (RRID:SCR_015293) Copy   

•   Source: SciCrunch Registry
  

http://www.norc.uab.edu

Research center that aims to understand the causal factors underlying nutrition and obesity-related health problems and the generation and evaluation of evidence on their consequences, prevention, and alleviation.

Proper citation: University of Alabama at Birmingham Nutrition and Obesity Research Center (RRID:SCR_015418) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://ftp.ncbi.nlm.nih.gov/pub/lu/LabeledIn/

Database of annotations of drug indications in FDA drug labels. LabeledIn contains an expert curated set of indications and a crowdsourced set of indications.

Proper citation: LabeledIn (RRID:SCR_015667) Copy   

•   Source: SciCrunch Registry
  

http://diseases.jensenlab.org/

Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence.

Proper citation: DISEASES (RRID:SCR_015664) Copy   

•   Source: SciCrunch Registry
  

https://www.cincinnatichildrens.org/research/divisions/n/nephrology/center-of-excellence

Center whose goal is to support basic, translational, and clinical research on critical pediatric kidney diseases by focusing on Acute Kidney Injury, Nephrotic Syndrome, and Lupus Nephritis.

Proper citation: Pediatric Centers of Excellence in Nephrology at Cincinnati Children's Hospital Medical Center (RRID:SCR_015302) Copy   

•   Source: SciCrunch Registry