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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

http://gentle.magnusmanske.de

Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more.

Proper citation: Gentle (RRID:SCR_016127) 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

https://www.icpsr.umich.edu/icpsrweb/content/addep/index.html

Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies.

Proper citation: Archive of Data on Disability to Enable Policy (ADDEP) (RRID:SCR_016315) Copy   

•   Source: SciCrunch Registry

https://nemoarchive.org/

Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.

Proper citation: NeMOarchive (RRID:SCR_016152) Copy   

•   Source: SciCrunch Registry

https://github.com/Sung-Huan/ANNOgesic

Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.

Proper citation: ANNOgesic (RRID:SCR_016326) Copy   

•   Source: SciCrunch Registry

http://hyphy.org/

Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.

Proper citation: HyPhy (RRID:SCR_016162) Copy   

•   Source: SciCrunch Registry

https://www.microsoft.com/en-gb/

Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.

Proper citation: Microsoft Excel (RRID:SCR_016137) Copy   

•   Source: SciCrunch Registry

http://www.cycif.org/

Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence.

Proper citation: CycIF.org (RRID:SCR_016267) Copy   

•   Source: SciCrunch Registry

https://github.com/alesssia/YAMP

Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability.

Proper citation: YAMP (RRID:SCR_016236) Copy   

•   Source: SciCrunch Registry

https://github.com/G-Node/nix/wiki

Software that defines a data model for annotated scientific datasets. It includes data together with metadata, and a corresponding file format based on HDF5 for storing and sharing such datasets.

Proper citation: NIX (RRID:SCR_016196) Copy   

•   Source: SciCrunch Registry

http://uthscsa-imagetool.software.informer.com/

Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images.

Proper citation: UTHSCSA ImageTool (RRID:SCR_016208) Copy   

•   Source: SciCrunch Registry

https://www.xlstat.com/en/

Software for commercial data analysis and statistical software package for Microsoft Excel.

Proper citation: XLSTAT (RRID:SCR_016299) Copy   

•   Source: SciCrunch Registry

https://github.com/Teichlab/tracer

Software application for recovery of T cell receptor (TCR) data from single cell data. Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles.

Proper citation: TraCeR (RRID:SCR_016338) Copy   

•   Source: SciCrunch Registry

https://github.com/mikessh/migec

Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires.

Proper citation: migec (RRID:SCR_016337) Copy   

•   Source: SciCrunch Registry