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http://databrary.org/

Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data.

Proper citation: Databrary (RRID:SCR_010471) Copy   

•   Source: SciCrunch Registry

http://www.arrayserver.com/wiki/index.php?title=ArrayStudio_Online_Help

Software package which provides statistics and visualization for analysis of high dimensional quantification data including microarray or RTPCR data or Taqman data, genotype data including SNP or Copy Number data and Next Generation Sequencing data. Provides integrated environment for analyzing and visualizing high dimensional data.

Proper citation: Array Studio (RRID:SCR_010970) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/limma/

Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.

Proper citation: LIMMA (RRID:SCR_010943) Copy   

•   Source: SciCrunch Registry

http://homer.ucsd.edu/

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

Proper citation: HOMER (RRID:SCR_010881) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/geo/

Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.

Proper citation: Gene Expression Omnibus (GEO) (RRID:SCR_005012) Copy   

•   Source: SciCrunch Registry

http://www.brain-map.org

Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain.

Proper citation: Allen Institute for Brain Science (RRID:SCR_006491) Copy   

•   Source: SciCrunch Registry

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https://github.com/spm

Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.

Proper citation: SPM (RRID:SCR_007037) Copy   

•   Source: SciCrunch Registry

http://harvester.fzk.de/harvester/

Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013.

Proper citation: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology (RRID:SCR_008017) Copy   

•   Source: SciCrunch Registry

https://nidagenetics.org/

Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website.

Proper citation: National Institute on Drug Abuse Center for Genetic Studies (RRID:SCR_013061) Copy   

•   Source: SciCrunch Registry

http://boinc.berkeley.edu

Software to orchestrate the distribution of computational work units (data and applications) to volunteers and have results collected back. It supports diverse applications, including those with large storage or communication requirements, and addresses unsolved issues in biology, medicine, physics, astronomy and computer science.

Proper citation: BOINC - Berkeley Open Infrastructure for Network Computing (RRID:SCR_015896) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/redcap-importer

Software that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import.

Proper citation: redcap-importer (RRID:SCR_016032) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/Bio-Tradis

Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.

Proper citation: Bio-tradis (RRID:SCR_015993) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/FIONASITE

Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive.

Proper citation: FIONASITE (RRID:SCR_016012) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/Minimally-Processed-Image-Sharing

Software to share ABCD minimally processed data. It uploads minimally-processed MRI data to the NDA ( Non-Disclosure Agreement) ABCD (Adolescent Brain Cognitive Development) repository.

Proper citation: Minimally-Processed-Image-Sharing (RRID:SCR_016016) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/Fast-Track-Image-Sharing

Software for sharing the ABCD (Adolescent Brain Cognitive Development) study data on the National Data Archive (NDA).

Proper citation: Fast-Track-Image-Sharing (RRID:SCR_016021) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/eprime-data-clean

Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests.

Proper citation: eprime-data-clean (RRID:SCR_016020) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/geocoding

Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude.

Proper citation: geocoding (RRID:SCR_016007) Copy   

•   Source: SciCrunch Registry

http://biopp.univ-montp2.fr/wiki/index.php/Main_Page

Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bio++ (RRID:SCR_016055) Copy   

•   Source: SciCrunch Registry

https://github.com/thegenemyers/DAZZ_DB

Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data.

Proper citation: Dazzler (RRID:SCR_016069) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/DEAP

Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States.

Proper citation: DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) Copy   

•   Source: SciCrunch Registry