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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
http://structuralbiology.cau.edu.cn/PlantGSEA/
Websever for gene set enrichment analysis of plants. Used for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets.
Proper citation: PlantGSEA (RRID:SCR_016866) Copy
Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES).
Proper citation: mqtldb (RRID:SCR_018002) Copy
Atlas is set of interactive tools built to promote retrieval, exploration, discovery, and analysis of Kidney Precision Medicine Project data by greater research community. Datasets available in repository are combination of raw and processed data from KPMP participant biopsies and reference tissue samples.
Proper citation: Kidney Tissue Atlas (RRID:SCR_021626) Copy
http://www.nmr.mgh.harvard.edu/DOT/resources/homer2/home.htm
Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data.
Proper citation: Homer2 (RRID:SCR_009586) Copy
http://dsi-studio.labsolver.org
A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system.
Proper citation: DSI Studio (RRID:SCR_009557) Copy
Software toolbox for data processing and analysis of brain imaging, evolved from DPARSF (Data Processing Assistant for Resting-State fMRI).
Proper citation: DPABI (RRID:SCR_010501) Copy
International biobank storing whole blood and DNA from 200,000 individuals, serum and plasma samples from more than 100,000 individuals as well as urine, RNA tubes, cells, buffy coat and Na-heparin tubes for environmental analysis for as many as 50,000 individuals. All bio-specimens from the HUNT surveys are collected, processed and stored at the HUNT Biobank in Levanger. The National CONOR Biobank is located on the same site, where it serves as a central research repository for DNA samples from all the largest Norwegian health surveys. These make up the Cohorts of Norway (CONOR), which include samples from more than 200,000 individuals. * HUNT 1 was carried out in 1984-1986 to establish the health history of 75,000 people. * HUNT 2, carried out in 1995-1997, focused on the evolution of the health history of 74,000 people. This included blood sample collection from 65,000 people. The data that accompany biospecimens in the biobank are stored in secured computer systems that run complex database management and analysis software. * HUNT 3 was completed in June 2008. 93,210 people were invited to participate in the study, and as of the 6th of June, 2008, 48,289 people participated (52% participation rate). The data, collected by means of questionnaires, interviews, clinical examinations and collection of blood and urine samples, will be ready for analysis in January 2009. * Young-HUNT is the adolescent part of HUNT including participants aged 13-19 years. Young-HUNT1 (1995-97) was conducted as part of HUNT2, 9141 adolescents participated (90% response rate). Young-HUNT2 (2000-01) was a follow-up study of Young-HUNT1, 2400 students participated in both studies (77% of the invited). Young-HUNT3 (2006-08) was a new cross-sectional study as part of HUNT3. This time 8677 adolescents participated (87% response rate). Data collection included self-reported questionnaires, structured interviews, clinical measurements and, in Young-HUNT3, buccal smears. All institutions with research expertise can apply for access to analyze HUNT data. Projects must have recommendations from The Regional Committee for Medical Research in Norway (REK) and be registered with The Norwegian Social Science Data Services (NSD).
Proper citation: Hunt Biobank (RRID:SCR_010626) Copy
https://github.com/facebook/prophet
Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton.
Proper citation: Prophet (RRID:SCR_017083) Copy
http://regent.qc.ca/assets/winrhizo_software.html
Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots.
Proper citation: WinRHIZO (RRID:SCR_017120) Copy
https://github.com/neuropoly/qMRLab
Software for quantitative MR image analysis, simulation, and protocol optimization. It aims to provide the community with a tool for data fitting, plotting, simulation and protocol optimization for a variety of different quantitative models.
Proper citation: qMRLab (RRID:SCR_016256) Copy
Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation.
Proper citation: HMS LINCS Center (RRID:SCR_016370) Copy
https://www.med.upenn.edu/cbica/captk/
Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.
Proper citation: Cancer Imaging Phenomics Toolkit (RRID:SCR_017323) Copy
Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.
Proper citation: hMRI-toolbox (RRID:SCR_017682) Copy
https://www.mbfbioscience.com/stereo-investigator-cleared-tissue-edition
Software tool for unbiased stereology to be used on cleared tissue. Used to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Includes number, length, area and volume analyses.
Proper citation: Stereo Investigator - Cleared Tissue Edition (RRID:SCR_017668) Copy
Platform provides resources for genomic observations from collection to analysis and publication. Works with standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets. Biocode Commons is also collaborating on development of Biological Collections Ontology, working to better integrate ontologies, vocabularies, and relevant standards that are related to BCO.
Proper citation: Biocode Commons (RRID:SCR_024553) Copy
https://www.mirion.com/products/genie-2000-basic-spectroscopy-software
Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data.
Proper citation: Genie 2000 Basic (RRID:SCR_021933) Copy
A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.
Proper citation: ToppCluster (RRID:SCR_001503) Copy
https://github.com/QMICodeBase/TORTOISEV4
An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.
Proper citation: TORTOISE (RRID:SCR_001645) Copy
https://github.com/sansomlab/tenx
Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis.
Proper citation: tenx (RRID:SCR_016957) Copy
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