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http://incelldownload.gehealthcare.com/bin/download_data/SoftWoRx/7.0.0/SoftWoRx.htm

Software for acquisition, deconvolution, processing, analysis, and display of DeltaVision images. Used in DeltaVision OMX SR imaging system., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SoftWoRx software (RRID:SCR_019157) Copy   

•   Source: SciCrunch Registry

http://easybioai.com/sc2disease/

Manually curated database of single cell transcriptome for human diseases. scRNA-seq database derived from numerous human studies. Provides researchers with encyclopedia of biomarkers at level of genes, cells, and diseases.

Proper citation: SC2diseases (RRID:SCR_019093) Copy   

•   Source: SciCrunch Registry

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

Software tool as deep collaborative learning with application to study of multimodal brain development. Uses deep network to represent original data and then seeks their correlations, while also linking data representation with phenotypical information.

Proper citation: Deep Collaborative Learning (RRID:SCR_019258) Copy   

•   Source: SciCrunch Registry

https://github.com/constantAmateur/SoupX

Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data.

Proper citation: SoupX (RRID:SCR_019193) Copy   

•   Source: SciCrunch Registry

https://github.com/datatagsuite

Software suite to enable discoverability of datasets. Enables submission of metadata on datasets to DataMed. Has core set of elements, which are generic and applicable to any type of dataset, and extended set that can accommodate more specialized data types. Platform independent model developed by NIH BD2K bioCADDIE project for DataMed Data Discovery Index prototype being developed. Also available as annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex.

Proper citation: DatA Tag Suite (RRID:SCR_019236) Copy   

•   Source: SciCrunch Registry

http://www.bionet.nsw.gov.au/

Repository for biodiversity data products managed by Department of Planning, Industry and Environment, New South Wales, Australia. It stores species sightings, systematic surveys, threatened biodiversity records and species names.

Proper citation: NSW BioNet (RRID:SCR_019162) Copy   

•   Source: SciCrunch Registry

https://www.addgene.org/collections/covid-19-resources/

Collections of Addgene plasmids, open access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists. Ordering or depositing plasmids related to COVID-19 research.

Proper citation: COVID-19 and Coronavirus plasmids and resources (RRID:SCR_018347) Copy   

•   Source: SciCrunch Registry

http://fit.genomics.lbl.gov/cgi-bin/myFrontPage.cgi

Web tool for browsing genome wide fitness experiments for diverse bacteria from Deutschbauer lab, the Arkin lab, and collaborators. Collection of mutant phenotypes for bacterial genes of unknown function.

Proper citation: Fitness Browser (RRID:SCR_018981) Copy   

•   Source: SciCrunch Registry

https://www.thegpm.org/crap/

List of proteins commonly found in proteomics experiments that are present either by accident or through unavoidable contamination of protein samples. List is based on analysis of current version of GPMDB, as well as suggestions by users. Current version of cRAP in FASTA format can be obtained from the GPM FTP site.

Proper citation: cRAP protein sequences (RRID:SCR_018187) Copy   

•   Source: SciCrunch Registry

https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/what-is-loupe-cell-browser

Desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Used to interrogate different views of 10x data to gain insights into underlying biology.

Proper citation: Loupe Browser (RRID:SCR_018555) Copy   

•   Source: SciCrunch Registry

https://covic.lji.org/

Consortium to unite efforts and resources from experts across globe to advance effective, antibody based therapies against novel coronavirus, SARS-CoV-2. Represents multidisciplinary convergence of structural biology, virologists, immunologists, clinicians and bioinformaticians from academic and industry settings. Collects antibodies for testing as part of CoVICS. Contributed antibodies are blinded and will only be known as code name. Antibody contributors will be able to see performance of their own molecules and take part in analysis. Contributors retain ownership of their antibodies and may continue to publish on them using original antibody names. Goal is to determine relative in vitro potency and in vivo efficacy using centralized standardized assays to identify best individual mAbs and rational combinations of mAbs. Consortium will recommend ideal therapeutic molecules for human use to protect vulnerable populations from COVID-19 disease. CoVIC database (CoVIC-DB) will serve as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them.

Proper citation: Coronavirus Immunotherapy Consortium (RRID:SCR_018258) Copy   

•   Source: SciCrunch Registry

https://metagenote.niaid.nih.gov/

Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository.

Proper citation: METAGENOTE (RRID:SCR_018494) Copy   

•   Source: SciCrunch Registry

http://himc.stanford.edu

Core designed for immune monitoring services for clinical and translational studies. Goals include providing standardized, state-of-the art immune monitoring assays at RNA, protein, and cellular level, testing and developing new technologies for immune monitoring, archive, report, and mine data from immune monitoring studies. HIMC uses online database for integration of data from standard HIMC assays, along with de-identified clinical and demographic data.

Proper citation: Stanford University Human Immune Monitoring Center Core Facility (RRID:SCR_018266) Copy   

•   Source: SciCrunch Registry

https://broadinstitute.github.io/warp/docs/Pipelines/Optimus_Pipeline/README

Optimus is a pipeline developed by the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA) Project that supports processing of any 3' single-cell and single-nuclei expression data generated with the 10x Genomic v2 or v3 assay. It is an alignment and transcriptome quantification pipeline that corrects cell barcodes, aligns reads to the genome, corrects Unique Molecular Identifiers (UMIs), generates an expression matrix in a UMI-aware manner, calculates summary metrics for genes and cells, detects empty droplets, returns read outputs in BAM format, and returns gene counts in NumPy matrix and Loom matrix formats.

Proper citation: Optimus Pipeline (RRID:SCR_018908) Copy   

•   Source: SciCrunch Registry

https://cluspro.bu.edu/

Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results.

Proper citation: ClusPro (RRID:SCR_018248) Copy   

•   Source: SciCrunch Registry

https://redivis.com

Commercial collaborative research platform for hosting and analyzing datasets.Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data.

Proper citation: Redivis (RRID:SCR_023111) Copy   

•   Source: SciCrunch Registry

https://brainiak.org

Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.

Proper citation: Brain Imaging Analysis Kit (RRID:SCR_014824) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/pearson-central-end-point

Data collection software as an end-point for centrally storing data from the Pearsons Q-Interactive.

Proper citation: pearson-central-end-point (RRID:SCR_016034) Copy   

•   Source: SciCrunch Registry

http://www.jstacs.de/index.php/GeMoMa

Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species.

Proper citation: GeMoMa (RRID:SCR_017646) Copy   

•   Source: SciCrunch Registry

https://github.com/BioDepot/BioDepot-workflow-builder

Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results.

Proper citation: BioDepot-workflow-builder (RRID:SCR_017402) Copy   

•   Source: SciCrunch Registry