Tools   Select Another Resource Report Type

http://viewer.shigen.info/cgi-bin/crispr/crispr.cgi

Web tool to show micro homology sequences striding over double strand break point created by CRISPR/Cas9 system. Used to search for CRISPR target site with micro-homology sequences. Used to predict deletion pattern.

Proper citation: NBRP Medaka CRISPR target site (RRID:SCR_018159) Copy   

•   Source: SciCrunch Registry

http://nucleobytes.com/index.php/4peaks

Software application for viewing and editing sequence trace files.

Proper citation: 4Peaks (RRID:SCR_000015) Copy   

•   Source: SciCrunch Registry

http://t2diacod.igib.res.in/

Gene atlas of Type 2 Diabetes Mellitus associated complex disorders. Provides curated and integrated information about genes involved in development and progression of Type 2 Diabetes Mellitus, genes and pathways with evidence for role in diabetes under risk factors including obesity, diet, inflammation, stress and complex disorders that are associated with Type 2 Diabetes Mellitus including atherosclerosis, diabetic retinopathy, diabetic nephropathy, diabetic neuropathy, cardiovascular disease.

Proper citation: T2DiACoD (RRID:SCR_019092) Copy   

•   Source: SciCrunch Registry

https://mzmatch.sourceforge.net/MetAssign.php

Software that combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download.

Proper citation: MetAssign (RRID:SCR_000092) Copy   

•   Source: SciCrunch Registry

http://cisbp.ccbr.utoronto.ca

Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.

Proper citation: CIS-BP (RRID:SCR_017236) Copy   

•   Source: SciCrunch Registry

https://www.fastgenomics.org/

Open online platform for single cell RNA-seq. Provides data management and analytics. Used to analyze public and private datasets and you can choose between several best practices workflows and browse existing analyses.

Proper citation: FASTGenomics (RRID:SCR_022898) Copy   

•   Source: SciCrunch Registry

https://www.robotreviewer.net/

Software tool as machine learning system that automatically assesses bias in clinical trials. From PDF formatted trial report determines risks of bias for domains defined by Cochrane Risk of Bias (RoB) tool, and extracts supporting text for these judgments.

Proper citation: Robot Reviewer (RRID:SCR_018961) Copy   

•   Source: SciCrunch Registry

https://www.estimationstats.com/#/

Web application for data analysis and visualizing effect sizes. Data analysis with estimation graphics.

Proper citation: Estimation Stats (RRID:SCR_018321) Copy   

•   Source: SciCrunch Registry

https://hcup-us.ahrq.gov/nisoverview.jsp

Family of healthcare databases and related software tools and products developed through Federal-State-Industry partnership. Databases bring together data collection of State data organizations, hospital associations, private data organizations, and Federal government to create national information resource of encounter-level healthcare data. HCUP includes largest collection of longitudinal hospital care data in the United States, with all-payer, encounter-level information beginning in 1988. These databases enable research on broad range of health policy issues, including cost and quality of health services, medical practice patterns, access to healthcare programs, and outcomes of treatments at the national, State, and local market levels.

Proper citation: Healthcare Cost and Utilization Project (RRID:SCR_024410) Copy   

•   Source: SciCrunch Registry

http://www.nihtoolbox.org/WhatAndWhy/Cognition/Language/Pages/NIH-Toolbox-Picture-Vocabulary-Test.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A measure of receptive vocabulary that is administered in a computerized adaptive format. The respondent is presented with an audio recording of a word and four photographic images on the computer screen and is asked to select the picture that most closely matches the meaning of the word. This test takes approximately 4 minutes to administer and is recommended for ages 3-85.

Proper citation: NIH Toolbox Picture Vocabulary Test (RRID:SCR_000166) Copy   

•   Source: SciCrunch Registry

http://s-quest.bihealth.org/fiddle/

Software interactive tool to help researchers to identify most appropriate publication format for their dataset that may be hard to publish in traditional journals. Formats include data repositories, micropublications, preprints, data journals, publishing platforms and journals that are open to null results. Users can search for publication format that meets their needs, compare and contrast formats, and find links to publishers. Open source tool to combat publication bias by getting research out of file drawer and into scientific community.

Proper citation: fiddle (RRID:SCR_017327) Copy   

•   Source: SciCrunch Registry

http://www.mrmatlas.org/

Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome.

Proper citation: SRMAtlas (RRID:SCR_016996) Copy   

•   Source: SciCrunch Registry

https://git.io/vAeKZ

It is non-graphical user interface in MATLAB which relies on keyboard callback functions. Used for analyzing big data sets.

Proper citation: ROIs selection with a non-graphical user interface (RRID:SCR_016352) Copy   

•   Source: SciCrunch Registry

http://apps.cytoscape.org/apps/pepper

A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...).

Proper citation: PEPPER (RRID:SCR_000431) Copy   

•   Source: SciCrunch Registry

https://figshare.com/articles/phi_toolbox_zip/3203326

Toolkit of MATLAB functions for computing integrated information ('phi' or 'Φ') from neural data. The toolbox consists of downloadable codes that perform practical computation.

Proper citation: Phi Toolbox (RRID:SCR_015549) Copy   

•   Source: SciCrunch Registry

http://www.humphreyslab.com/SingleCell/

Software tool as analyzer for kidney single cell datasets. Allows users to query gene expression from mouse or human kidney and human kidney organoid single cell datasets. For details about datasets visit ReBuilding a Kidney website.

Proper citation: Kidney Interactive Transcriptomics (RRID:SCR_017209) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/EGSEA/

Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets.

Proper citation: EGSEA (RRID:SCR_015036) Copy   

•   Source: SciCrunch Registry

https://as.nyu.edu/research-centers/cbi/resources/Software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software which converts DICOM images to NIfTI format.

Proper citation: dinifti (RRID:SCR_000303) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc/software/131-shapeworks.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results.

Proper citation: ShapeWorks (RRID:SCR_000424) Copy   

•   Source: SciCrunch Registry

Issue

https://cran.r-project.org/web/packages/adegenet/index.html

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

Proper citation: ADEGENET (RRID:SCR_000825) Copy   

•   Source: SciCrunch Registry