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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
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
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
https://github.com/kendomaniac/rCASC
Software package for reproducible classification analysis of single cell sequencing data.
Proper citation: rCASC (RRID:SCR_017005) Copy
Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis.
Proper citation: INCF-Neurobot (RRID:SCR_017004) Copy
https://www.stemformatics.org/#
Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data. Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others.
Proper citation: Stemformatics (RRID:SCR_017002) Copy
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
https://github.com/fenderglass/Flye
Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms.
Proper citation: Flye (RRID:SCR_017016) Copy
http://sourceforge.net/projects/bbmap
Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform.
Proper citation: BBmap (RRID:SCR_016965) Copy
http://zhoulab.usc.edu/TopDom/
Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TopDom (RRID:SCR_016964) Copy
http://cctop.enzim.ttk.mta.hu/
Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them.
Proper citation: CCTOP (RRID:SCR_016963) Copy
Web based ontology enrichment tool for lipidomic data analysis. Used for lipidomics to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and organelle associations. Freely accessible in a platform independent way.
Proper citation: LION/web (RRID:SCR_017018) Copy
Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows.
Proper citation: Anima (RRID:SCR_017017) Copy
Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC).
Proper citation: Illuminating the Druggable Genome (RRID:SCR_016924) Copy
https://commonfund.nih.gov/hubmap
Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows.
Proper citation: The Human BioMolecular Atlas Program (RRID:SCR_016922) Copy
Software tool as a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive . DEE2 consists of three parts: Webserver where end-users can search for and obtain data-sets of interest, Pipeline that can download and process SRA data as well as users own fastq files, Back-end that collects, filters and organises data provided by contributing worker nodes.
Proper citation: Digital Expression Explorer 2 Project (RRID:SCR_016929) Copy
http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3
Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches.
Proper citation: ALGGEN-PROMO (RRID:SCR_016926) Copy
ImageJ plug-in to quantify fibrillar structures in raw microscopy images. Used to evaluate the orientation of fiber orientation pattern and plots the results in the image.
Proper citation: FibrilTool (RRID:SCR_016773) Copy
https://github.com/ToolsVanBox/smMIPfil
Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required.
Proper citation: smMIPfil (RRID:SCR_016892) Copy
https://github.com/zitmen/thunderstorm
Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging.
Proper citation: Thunder STORM (RRID:SCR_016897) Copy
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