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https://hdmf.readthedocs.io/

Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data.

Proper citation: Hierarchical Data Modeling Framework (RRID:SCR_021303) Copy   

•   Source: SciCrunch Registry

https://rubygems.org/gems/viral_seq

Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis.

Proper citation: viral_seq (RRID:SCR_018515) Copy   

•   Source: SciCrunch Registry

https://github.com/ttrogers/DecodingDynamic

Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex.

Proper citation: DecodingDynamic (RRID:SCR_021099) Copy   

•   Source: SciCrunch Registry

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp

Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information.

Proper citation: CustomCDF (RRID:SCR_018527) Copy   

•   Source: SciCrunch Registry

http://www.msbioworks.com/

A protein mass spectrometry service provider that delivers data to industrial and government organizations as well as academic institutions. Protein services include protein identification, mapping, profiling, and mass measurement. Post-translational modification services include PTM profiling, phospho-screening, and glyco-screening. Quantitative proteomics services include workflows for label free, TMT, SILAC, and PRM. MS Bioworks also provides immunoprecipitated protein analysis and custom analysis.

Proper citation: MS Bioworks (RRID:SCR_001043) Copy   

•   Source: SciCrunch Registry

http://www.worm.mpi-cbg.de/phenobank/cgi-bin/ProjectInfoPage.py

A database that provides primary data from two high-content screens that profile the set of ~900 essential C. elegans genes (~5% of the genome) required for embryo production and/or events during the first two embryonic divisions. Phenobank houses the movies, scored defects, and phenotypic classification data for the embryo-filming and gonad morphology screens.

Proper citation: PhenoBank (RRID:SCR_000930) Copy   

•   Source: SciCrunch Registry

http://www.uniprot.org/

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Proper citation: UniProt (RRID:SCR_002380) Copy   

•   Source: SciCrunch Registry

https://view.qiime2.org/

Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided.

Proper citation: QIIME 2 View (RRID:SCR_018074) Copy   

•   Source: SciCrunch Registry

http://www.premierbiosoft.com/protein_quantification_software/index.html

Software package as comprehensive qualitative and quantitative suite for proteomics. Used to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. Provides customizable interface to support any form of biological annotation. Used to compare protein quantitative results in relation to biological pathways, protein localization, protein function, or to transcript abundance. Every protein identification can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or in-house LIMS.

Proper citation: PremierBiosoft Proteo IQ Software (RRID:SCR_018072) Copy   

•   Source: SciCrunch Registry

http://circadb.hogeneschlab.org/

Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans.

Proper citation: CircaDB (RRID:SCR_018078) Copy   

•   Source: SciCrunch Registry

http://www.milesculabs.org/QuB.html

Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: QuB (RRID:SCR_018076) Copy   

•   Source: SciCrunch Registry

https://vivli.org/

Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials.

Proper citation: Vivli (RRID:SCR_018080) Copy   

•   Source: SciCrunch Registry

http://www.diploid.com/moon

Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid.

Proper citation: MOON (RRID:SCR_018005) Copy   

•   Source: SciCrunch Registry

https://github.com/yousra291987/ChiCMaxima

Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling.

Proper citation: ChiCMaxima (RRID:SCR_018178) Copy   

•   Source: SciCrunch Registry

http://www.innovision-systems.com/Products/MaxTraq.html

Software package for motion capture analysis by Innovision Systems Inc.

Proper citation: MaxTRAQ (RRID:SCR_018188) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.fh-hagenberg.at/site/index.php?id=17

Software scoring system to identify peptides out of tandem mass spectrometry data using database of known proteins. Universal identification algorithm optimized for high resolution and high accuracy tandem mass spectra. Software tool as peptide and protein identification algorithm developed by Bioinformatics Research Group University of Applied Sciences Upper Austria in close cooperation with group of Karl Mechtler at IMP Vienna, Austria.

Proper citation: MS Amanda (RRID:SCR_018396) Copy   

•   Source: SciCrunch Registry

http://statistika.mfub.bg.ac.rs/interactive-dotplot/

Web-based tool to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of continuous variable across different study groups, visualization of subgroups or clusters of non-independent data. Web visualization tool for creating dot plots, box plots and violin plots for small sample size data sets.

Proper citation: Interactive Dotplot (RRID:SCR_018329) Copy   

•   Source: SciCrunch Registry

https://dice-database.org

Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis.

Proper citation: Database of Immune Cell Epigenomes (RRID:SCR_018259) Copy   

•   Source: SciCrunch Registry

https://biit.cs.ut.ee/gprofiler/page/r

Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool.

Proper citation: gProfiler2 (RRID:SCR_018190) Copy   

•   Source: SciCrunch Registry

https://sedfitsedphat.nibib.nih.gov/software/default.aspx

Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.

Proper citation: SEDFIT (RRID:SCR_018365) Copy   

•   Source: SciCrunch Registry