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https://sleepdata.org/datasets/abc

Portal for randomized controlled trial to compare effectiveness of bariatric surgery versus continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea. Signals included in the polysomnography (PSG) montage are EEG, EMG, EOG, ECG, SpO2, airflow, CPAP pressure, CPAP flow, plethysmography, position, pulse, light, respiratory effort, snore.

Proper citation: Apnea, Bariatric surgery, and CPAP study (RRID:SCR_016575) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/projects/mutagene/

Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity.

Proper citation: MutaGene (RRID:SCR_016574) Copy   

•   Source: SciCrunch Registry

https://www.bdbiosciences.com/en-us/products/instruments/flow-cytometers/research-cell-sorters/bd-facsaria-iii

Instrument for cell sorting by BD Biosciences where positive air pressure forces sample cell through an optically gel-coupled cuvette . Hydrodynamic focusing guides particles in a single-file stream through the cuvette, where laser light intercepts the stream at the sample interrogation point.Fluorescence activated cell sorting instrument. Flow cytometer as high speed fixed alignment benchtop cell sorter. Enables multicolor analysis of up to 13 fluorescent markers and two scatter parameters at time.

Proper citation: BD Biosciences: FACSAria III Cell Sorter (RRID:SCR_016695) Copy   

•   Source: SciCrunch Registry

http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home

Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools.

Proper citation: Appion Package (RRID:SCR_016734) Copy   

•   Source: SciCrunch Registry

https://niaid.github.io/dcas/

Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: dCAS (RRID:SCR_016612) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/workflows/html/RnaSeqGeneEdgeRQL.html

Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment.

Proper citation: RnaSeqGeneEdgeRQL (RRID:SCR_016699) Copy   

•   Source: SciCrunch Registry

http://grigoriefflab.janelia.org/ctffind4

Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4.

Proper citation: CTFFIND (RRID:SCR_016732) Copy   

•   Source: SciCrunch Registry

https://bioinformatics.niaid.nih.gov/nglycpred/

Web based server to discriminate between glycosylated and non-glycosylated N-X-(T/S) sequons by incorporating structural information and patterns.

Proper citation: NGlycPred (RRID:SCR_016610) Copy   

•   Source: SciCrunch Registry

https://github.com/NeurophysVis/SpectraVis

Web based neuroscience application for analyzing task-related functional networks over time and frequency. Interactive visualization tool for exploring functional brain connectivity.

Proper citation: SpectraVis (RRID:SCR_016691) Copy   

•   Source: SciCrunch Registry

https://bioinformatics.niaid.nih.gov/hasp

Web server to visualize phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of homology models. Database and structural visualization platform for comparative models of influenza A hemagglutinin proteins.

Proper citation: HASP (RRID:SCR_016615) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/ccshs

Portal for population based pediatric cohorts studied with objective sleep studies. Includes children with in-home sleep studies, acoustic reflectometry, anthropometry, spirometry, blood pressure (BP), and neuropsychology (NP) and behavioral assessments. Signals recorded include EEG, ECG, EOG, EMG, SpO2, airflow (thermocouple) nasal pressure, respiratory effort, position, plethysmography, light, HR.

Proper citation: Cleveland Children's Sleep and Health Study (RRID:SCR_016584) Copy   

•   Source: SciCrunch Registry

http://www.indecbiosystems.com/imagingworkbench/default.asp

Software for multichannel dynamic fluorescence image acquisition and analysis by INDEC BioSystems.

Proper citation: Imaging WorkBench (RRID:SCR_016589) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/bestair/

Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume.

Proper citation: Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) Copy   

•   Source: SciCrunch Registry

https://pachterlab.github.io/kallisto/about

Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads.

Proper citation: kallisto (RRID:SCR_016582) Copy   

•   Source: SciCrunch Registry

https://github.com/LabTranslationalArchitectomics/RiboWaltz

Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates.

Proper citation: riboWaltz (RRID:SCR_016948) Copy   

•   Source: SciCrunch Registry

https://www.apple.com/numbers/

Software tool to create spreadsheets that include tables and images. You can use Apple Pencil on your iPad to add diagrams and colorful illustrations.

Proper citation: Numbers (RRID:SCR_016950) Copy   

•   Source: SciCrunch Registry

https://github.com/tarokiritani/WhiskerTracking

ImageJ plugins and macros for whisker tracking. Set of Fiji plugins and macros for tracking a single whisker.

Proper citation: Whisker tracking macro (RRID:SCR_016953) Copy   

•   Source: SciCrunch Registry

https://affinity.serif.com/en-us/photo/

Software tool for professional photo editing.

Proper citation: Affinity Photo (RRID:SCR_016951) Copy   

•   Source: SciCrunch Registry

http://sciencedynamics.data4good.io

Portal for Science Dynamics projects with open source framework to provide way to query datasets. Code framework, including tutorials for project, titled Over Optimization of Academic Publishing Metrics Observing Goodhart Law in Action, to interactively explore and understand how various properties of journals have changed over time. Datasets, software implementations, code tutorials and interactive web interface for investigating studied networks.

Proper citation: Science Dynamics (RRID:SCR_016958) Copy   

•   Source: SciCrunch Registry

https://www.olympus-global.com/technology/museum/micro/2004/

FV1000 confocal laser scanning biological microscope features twin scan system which enables spectroscopy of living intercellular contents and analysis of objects down to a 2nm wavelength resolution. Image size is increased to 4096x4096 pixels.

Proper citation: Olympus: FV1000 Confocal Microscope (RRID:SCR_016840) Copy   

•   Source: SciCrunch Registry