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https://github.com/jtamames/SqueezeMeta
Software tool as fully automated pipeline for metagenomic analysis. Used for metagenomics covering all steps of analysis. Features several characteristics including co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of abundances of genes in each metagenome. Includes binning and bin checking for retrieving individual genomes.
Proper citation: SqueezeMeta (RRID:SCR_021821) Copy
https://circexplorer2.readthedocs.io/en/latest/
Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs.
Proper citation: CIRCexplorer2 (RRID:SCR_021664) Copy
https://bioconductor.org/packages/BASiCS/
Software tool for Bayesian analysis of single cell sequencing data. Used to perform statistical analyses of single cell RNA sequencing datasets in context of supervised experiments.
Proper citation: Bayesian Analysis of Single Cell Sequencing (RRID:SCR_021829) Copy
Software tool used to plot circular plots and visualize genomic data along genomic locations.
Proper citation: Circa (RRID:SCR_021828) Copy
https://scicrunch.org/ResourceWatch
Knowledgebase of biomedical research resources. Repository for storing validation and problematic information about variety of entities within biomedical domain, such as antibodies, cell lines, etc. Enables researchers to submit their own claims about specific entity to make validation/problematic information F.A.I.R. (Findable, Accessable, Interoperable, Reuseable).
Proper citation: Biomed Resource Watch (RRID:SCR_021761) Copy
Platform for recognizing and promoting Open Research. Open online service that aims to offer fairer and more democratic platform for recognizing researcher contributions.Allows researchers to openly acknowledge colleagues for meaningful contributions to research process, such as Publication, Mentoring,Teaching,Data sharing,Reproducibility practices, Sharing negative results, Participation in discussion groups,Software development, Clinical trials management, Leadership, Community outreach, Public engagement. ORCID iDs, DOIs, grant IDs and other persistent identifiers are used where available as links to appropriate contributions.
Proper citation: Rescognito (RRID:SCR_021874) Copy
https://sourcemd.toolforge.org/index_old.php
Web tool as prototype service to automatically generate Wikidata items using metadata from scholarly publications. Citation lookup tool in Wikipedia platform. Takes persistent identifier for scholarly article and processes it by importing bibliographic metadata into Wikidata items. In August 2018, it was merged with ORCIDator into single tool that allows for fully automated batch processing based on ISBN-13, DOI, ORCID iD, PubMed ID, PMCID identifiers.
Proper citation: SourceMD (RRID:SCR_021633) Copy
https://services.healthtech.dtu.dk/service.php?NetMHC-4.0
Web tool for binding prediction of peptides to MHC class I molecules. The newest version NetMHC- 4.0 is used for prediction of peptide MHC class I binding affinity using gapped sequence alignment that allows insertions and deletions in alignment.
Proper citation: NetMHC (RRID:SCR_021651) Copy
https://www.zeiss.com/microscopy/int/products/microscope-software/labscope.html
Software tool for image acquisition using WiFi-enabled Zeiss microscopes. Compatible with Windows PCs and with Apple tablets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Zeiss LabScope (RRID:SCR_021768) Copy
https://sites.cscc.unc.edu/aric/
Platform for prospective epidemiologic study conducted in four U.S. communities. One of most significant and longest running heart health studies and is the largest study of heart health in African Americans. ARIC investigates risk factors for heart disease and stroke, and connections between cardiovascular and cognitive health. ARIC includes two parts: Cohort Component and Community Surveillance Component. Cohort Component began in 1987, and each ARIC field center randomly selected and recruited cohort sample of individuals aged 45-64 from defined population in their community, to receive extensive examinations, including medical, social, and demographic data. In Community Surveillance Component, four communities are investigated to determine long term trends in hospitalized myocardial infarction and coronary heart disease deaths in men and women aged 35-84 years.
Proper citation: Atherosclerosis Risk in Communities (RRID:SCR_021769) Copy
Website devoted to papers that contain machine learning datasets, code, methods and evaluation tables. Done together with community, supported by NLP and ML.All content on this website is openly licenced under CC-BY-SA and everyone can contribute.Also operates specialized portals for papers with code in astronomy, physics, computer sciences, mathematics and statistics.
Proper citation: Papers with Code (RRID:SCR_021800) Copy
https://www.ionoptix.com/products/software/ionwizard-core-and-analysis/
Software tool to perform rapid fluorescence and morphometric real time, synchronous data acquisition with IonOptix systems, as well as polynomial fitting and analysis for myocyte research. Features include data trace averaging and filtering,composite images, and transient analysis. Integrates presentation of fluorescence traces and images, analog voltages, and cell length data under intuitive interface. Analyzes raw data by performing ratio, ion, or linear calibration calculations.
Proper citation: IonWizard (RRID:SCR_021764) Copy
https://cumulus.readthedocs.io/en/stable
Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.
Proper citation: Cumulus (RRID:SCR_021644) Copy
https://knowledge.figshare.com/plus
Web based interface designed for academic research data management and research data dissemination. Accepts all file types. Enables academics to upload, share, cite and discover all manner of research outputs with security of knowing our hosting options and platform support long term preservation of data.Used to share big datasets from 100GB up. Added features and expert guidance are also included for sharing your data FAIR-ly.During data deposit, personal email support is available and once submitted, Figshare data expert will conduct review of the metadata and spot check of your dataset files and offer guidance, with main aim of enhancing discoverability and reusability.
Proper citation: FigsharePlus (RRID:SCR_021762) Copy
https://www.trikinetics.com/Downloads/DAMSystem3%20Software%20Data%20Sheet.pdf
Software tool for data collection to upload output from set of activity monitors and periodically saves it in disk files on Macintosh or Windows PC. Part of TriKinetics Drosophila Activity Monitoring System.
Proper citation: TriKinetics DAMSystem3 Software (RRID:SCR_021809) Copy
https://github.com/jeffdaily/parasail
Software tool as multiple sequence alignement for global, local and semi global alignments.
Proper citation: PARASAIL (RRID:SCR_021805) Copy
http://www.lbgi.fr/~julie/LEON-BIS
Software tool for sequence alignments evaluation. Multiple alignment evaluation of sequence neighbours using Bayesian inference system. Used to distinguish sections in multiple sequence alignments that are conserved across whole family or within subfamilies, and should be useful for automatic, high-throughput genome annotations, 2D/3D structure predictions, protein-protein interaction predictions etc.
Proper citation: LEON BIS (RRID:SCR_021803) Copy
http://www.glycosciences.de/tools/linucs/
Service that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form. Input: A structure using the extended, non-graphic nomenclature (in ASCII writing) to describe complex carbohydrates as recommended by IUPAC. Output: A linear, unique notation. The source code (written in C), will be distributed so that software developers can easily implement their algorithm within their own application. LINUCS was chosen to fulfill to following conditions: * Input of extended, non-graphic nomenclature to describe carbohydrate structures. * Resulting linear code is closely related to notations and abbreviations recommended by IUPAC. * Number of additional rules to define the priority of the branches is low * Extended nomenclature of complex carbohydrates contains all information to define the hierarchy. * LINUCS is applicable to all types of carbohydrates (macrocyclic system are currently not implemented) . * Remaining unassigned linkage information are tolerated
Proper citation: LINUCS (RRID:SCR_001571) Copy
A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.
Proper citation: cpnDB: A Chaperonin Database (RRID:SCR_002263) Copy
Portal that provides multimedia educational content from courses, conference lectures, and laboratory exercises from some of leading neuroscience institutes and societies to be more accessible to global neuroscience community.
Proper citation: TrainingSpace (RRID:SCR_022036) Copy
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