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https://www.ebi.ac.uk/ena/pathogens/covid-19

Data collection related to COVID-19 held at EMBL-EBI , including sequences of outbreak isolates and records related to coronavirus biology, protein expression, protein sequence, protein structure, proteome and translatome data and literature.

Proper citation: EMBL-EBI Pathogens - COVID-19 (RRID:SCR_018343) Copy   

•   Source: SciCrunch Registry

https://bigd.big.ac.cn/ncov/?lang=en

Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data.

Proper citation: 2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation (RRID:SCR_018342) Copy   

•   Source: SciCrunch Registry

http://www.evolvedmicrobe.com/CurveFitter/

Software tool for growth curve fitting and visualization. Program allows to fit growth curve using simple GUI or advanced scripting environment. Used to fit growth curves generated for data collected in microtiter plates or elsewhere.

Proper citation: CurveFitter (RRID:SCR_018461) Copy   

•   Source: SciCrunch Registry

https://github.com/embl-cba/fiji-plugin-bigDataProcessor/blob/master/README.md

Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy.

Proper citation: Big Data Processor (RRID:SCR_018484) Copy   

•   Source: SciCrunch Registry

http://theparkerlab.org/tools/isleteqtl/

Web tool for exploring variants in islet expression quantitative trait loci. Data is result of collaboration between Michigan University Parker lab, Department of Biostatistics and Center for Statistical Genetics at University of Michigan, National Human Genome Research Institute, Jackson Laboratory for Genomic Medicine, Department of Genetics at University of North Carolina, European Bioinformatics Institute, Department of Preventive Medicine at University of Southern California, and Department of Physiology and Biophysics at University of Southern California.

Proper citation: Islet eQTL Explorer (RRID:SCR_018692) Copy   

•   Source: SciCrunch Registry

https://www.ucl.ac.uk/ncl-disease/mutation-and-patient-database

Collection of published mutations and sequence variations in genes that cause Neuronal Ceroid Lipofuscinoses together with unpublished data included with permission. There are two tables for each human NCL disease gene - Patient Datasheets list all published or reported patients and families, and Mutation Datasheets list all published or reported mutations, cross-referenced to patient table. Datasheets are available to view or download as excel files for off-site use to aid local needs or interests. Database follows mutation nomenclature recommendations of Human Genome Variation Society.

Proper citation: Mutation and Patient Database (RRID:SCR_018806) Copy   

•   Source: SciCrunch Registry

https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/

Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data.

Proper citation: RiboTaper (RRID:SCR_018880) Copy   

•   Source: SciCrunch Registry

http://had.co.nz/reshape/

Software R package for flexibly restructuring and aggregating data.

Proper citation: reshape (RRID:SCR_018983) Copy   

•   Source: SciCrunch Registry

http://annotree.uwaterloo.ca/

Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes.

Proper citation: Annotree (RRID:SCR_018980) Copy   

•   Source: SciCrunch Registry

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

https://github.com/auranic/ClinTrajan

Software Python package for analysis of trajectories in clinical datasets.

Proper citation: ClinTrajAn (RRID:SCR_019018) 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://rapps.hirnetwork.org/scPancMeta/

Portal for islet research community. Data for eight scRNA-seq datasets are combined to give consensus overview of islet cell type defining genes. Tools are provided for interacting with and comparing novel genesets generated.

Proper citation: scPancMeta App (RRID:SCR_018939) Copy   

•   Source: SciCrunch Registry

https://cftr2.org/

International initiative led by team of researchers and clinicians and supported by the US Cystic Fibrosis Foundation that seeks to provide complete, advanced and expert reviewed functional and clinical information on CFTR mutations. Provides information for patients, researchers, and general public about specific variants. For each variant or variant combination included in database, website will provide information about whether variant or variant combination is CF-causing, and information about sweat chloride, lung function, pancreatic status, and Pseudomonas infection rate in patients in CFTR2 database with this variant or variant combination.

Proper citation: CFTR2 (RRID:SCR_019078) 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://github.com/ShaokunAn/D-EE

Software tool for distributed dimensionality reduction and visualization. Distributed software for visualizing intrinsic structure of large scale single cell data written in C language. Its distributed storage and distributed computation technique allows efficiently analyze large scale single cell data at cost of constant time speedup.

Proper citation: D-EE (RRID:SCR_019058) Copy   

•   Source: SciCrunch Registry

http://physionet.org/physiobank/

Archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. The PhysioBank Archives now contain over 700 gigabytes of data that may be freely downloaded. PhysioNet is seeking contributions of data sets that can be made freely available in PhysioBank. Contributions of digitized and anonymized (deidentified) physiologic signals and time series of all types are welcome. If you have a data set that may be suitable, please review PhysioNet''s guidelines for contributors and contact them.

Proper citation: Physiobank (RRID:SCR_006949) Copy   

•   Source: SciCrunch Registry

https://www.axionbiosystems.com/products/software/neural-module

Neural Module by Axion BioSystems Inc, provides simplified approach to set up, execution and analysis of neural experiments. Enables Maestro Pro and Edge to record and analyze key parameters of neural network function, including activity, synchrony, and network oscillations.

Proper citation: Neural Module (RRID:SCR_019270) 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