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https://www.objtables.org

Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.

Proper citation: ObjTables (RRID:SCR_018652) Copy   

•   Source: SciCrunch Registry

https://github.com/chris-mcginnis-ucsf/DoubletFinder

Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data.

Proper citation: DoubletFinder (RRID:SCR_018771) Copy   

•   Source: SciCrunch Registry

https://rosie.graylab.jhu.edu/docking2

Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community.

Proper citation: ROSIE (RRID:SCR_018764) Copy   

•   Source: SciCrunch Registry

http://datasets.datalad.org/

DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data.

Proper citation: datasets.datalad.org (RRID:SCR_019089) Copy   

•   Source: SciCrunch Registry

https://run.biosimulations.org

Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource.

Proper citation: runBioSimulations (RRID:SCR_019110) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001096/

Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences.

Proper citation: MITE-Hunter (RRID:SCR_020946) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/hisat2/index.shtml

Graph-based alignment of next generation sequencing reads to a population of genomes.

Proper citation: HISAT2 (RRID:SCR_015530) Copy   

•   Source: SciCrunch Registry

http://www.iu.edu/~beca/

Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.

Proper citation: BECA (RRID:SCR_015846) Copy   

•   Source: SciCrunch Registry

http://avogadro.cc/

Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Proper citation: Avogadro (RRID:SCR_015983) Copy   

•   Source: SciCrunch Registry

https://github.com/Mark-Kramer/Seizure-Waves

Analysis and modeling code for waves of seizure activity.

Proper citation: Seizure-Waves (RRID:SCR_017455) Copy   

•   Source: SciCrunch Registry

http://qutublab.rice.edu/cytoNet/

Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory.

Proper citation: cytoNet (RRID:SCR_017465) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/ChromHMM/

Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.

Proper citation: ChromHMM (RRID:SCR_018141) Copy   

•   Source: SciCrunch Registry

http://raptorx.uchicago.edu/

Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model.

Proper citation: RaptorX (RRID:SCR_018118) Copy   

•   Source: SciCrunch Registry

http://ultrascan.aucsolutions.com/

Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis.

Proper citation: UltraScan (RRID:SCR_018126) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/reprocontainers/

Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments.

Proper citation: ReproNim/containers (RRID:SCR_018467) Copy   

•   Source: SciCrunch Registry

https://github.com/mourisl/Rcorrector

Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads.

Proper citation: Rcorrector (RRID:SCR_022011) Copy   

•   Source: SciCrunch Registry

https://github.com/Benson-Genomics-Lab/TRF

Software tool to locate and display tandem repeats in DNA sequences. Program to analyze DNA sequences.

Proper citation: Tandem Repeats Finder (RRID:SCR_022193) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/MashMap

Software tool as fast approximate aligner for long DNA sequences. Used for computing local alignment boundaries between long DNA sequences.

Proper citation: MashMap (RRID:SCR_022194) Copy   

•   Source: SciCrunch Registry

http://www.geosamples.org/

Sample Catalog and Registry for the International Geo Sample Number. SESAR catalogs and preserves sample metadata profiles, and provides access to the sample catalog via the Global Sample Search.

Proper citation: System for Earth Sample Registration (RRID:SCR_002222) Copy   

•   Source: SciCrunch Registry

http://nsidc.org/agdc/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. Archives and distributes Antarctic glaciological and cryospheric system data collected by the U.S. Antarctic Program. The Data Catalog contains data sets collected by individual investigators and products assembled from many different PI data sets, published literature, and other sources. The catalog provides useful compilations of important geophysical parameters, such as accumulation rate or ice velocity. The NSF OPP Guidelines and Award Conditions for Scientific Data state that PIs should submit data collected as a result of their OPP grant to a designated data center as soon as possible, but no later than two years after the data are collected.

Proper citation: Antarctic Glaciological Data Center (RRID:SCR_002219) Copy   

•   Source: SciCrunch Registry