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https://github.com/open2c/pairtools
Software command line framework to process sequencing data from Hi-C experiment. Used to process pair end sequence alignments.
Proper citation: pairtools (RRID:SCR_023038) Copy
https://github.com/hartwigmedical/hmftools/blob/master/purple/README.md
Software tool as purity ploidy estimator for whole genome sequenced data. Used for copy number calling and determination of sample purity.
Proper citation: PURPLE (RRID:SCR_022999) Copy
Software to visualize and qualitatively analyze mass spectrometry data. Used to display chromatograms and spectra, detect and integrate chromatographic peaks, search mass spectral libraries, simulate mass spectra, subtract background spectra, apply scan filters, annotate plots with text and graphics, create and save layouts, view the status of various instrument parameters during data acquisition, and create a 2D or 3D representation of an analysis displaying the acquired mass/wavelength scans. Part of liquid chromatography mass spectrometry system.
Proper citation: FreeStyle 1.8 SP1 (RRID:SCR_022877) Copy
https://github.com/walaj/svaba
Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements.
Proper citation: SvABA (RRID:SCR_022998) Copy
http://www.brainhealthdatabank.ca
Repository of many types and sources of data including, but not limited to, assessments, imaging, wearable, and biological samples, collected from research projects at the Centre for Addiction and Mental Health. Data that individuals choose to share to advance mental health.
Proper citation: BrainHealth Databank (RRID:SCR_022996) Copy
Organization to optimize the care of women, men, and children with lower urinary tract dysfunction and/or pelvic floor disorders through education, research and involvement in health care policy. To improve the art and science of Urology through basic and applied clinical research in urodynamics and neurourology, voiding function and dysfunction, female urology and pelvic floor dysfunction, and to disseminate and teach these concepts.
Proper citation: Society of Urodynamics, Female Pelvic Medicine and Urogenital Reconstruction (SUFU) (RRID:SCR_022874) Copy
Research and education program in Harvard Program in Therapeutic Science at Harvard Medical School to advance science and to develop technology needed to accelerate invention of new medicines and personalization of patient care. Used to study molecular causes of disease, ways drugs exert their therapeutic and adverse effects, design and interpretation of clinical trials.
Proper citation: Laboratory of Systems Pharmacology program (RRID:SCR_022873) Copy
https://www.pinnaclet.com/sleepPRO.html
Software tool to reduce scoring time and simplify data analysis. Offers automated power analysis, semi-automated scoring methods, and advanced tabular and graphical analysis for investigating sleep data sets. Custom scoring and analysis are also available. Scoring sessions between two or more users can be compared. All EEG/EMG and video data sets recorded with Pinnacle software, as well as third party EDF files, can be imported.
Proper citation: Sirenia Sleep Pro (RRID:SCR_022918) Copy
https://www.genoscope.cns.fr/brassicanapus/
Web tool as Brassica napus genome browser.
Proper citation: CNS Genoscope (RRID:SCR_023020) Copy
https://github.com/c-zhou/yahs
Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies.
Proper citation: YaHS (RRID:SCR_022965) Copy
https://www.iveindhoven.com/en/article/reichert-jung-ultracut-e-ultramicrotome/
Reichert Jung Ultracut E, article number 131-960, is used to cut ultrathin and semithin sections of resin embedded samples for electron microscopy.
Proper citation: Ultracut: E ultramicrotome (RRID:SCR_022980) Copy
Software suite to analyse gait trials collected with Experimental Dynamic Gait Arena for Rodents. Used for rodent gait analysis.
Proper citation: GAITOR Suite (RRID:SCR_023031) Copy
The Precellys 24 homogenizer with automatic tube locking system with the ability to process up to 24 tubes simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Bertin Technologies: Precellys 24 tissue homogenizer (RRID:SCR_022979) Copy
https://www.emkatech.com/product/iox2-software/
Software tool to acquire, analyze, view, and store physiological data generated during preclinical experiment. Has library of application specific analysis modules for real time signal processing.
Proper citation: IOX2 (RRID:SCR_022973) Copy
https://www.inscopix.com/nvoke
Miniature microscope system that integrates in vivo cellular resolution calcium imaging with simultaneous or sequential optogenetic manipulation to causally link neural circuit activity with behavior.
Proper citation: iNSCOPIX: nVoke System (RRID:SCR_023028) Copy
https://open-brain-consent.readthedocs.io/en/stable/
Platform for informing research participants and obtaining consent to share brain imaging data. Provides suggested wording/templates for MRI studies human participant consent forms (including GDPR version), reference of tools for data anonymization, etc to make prospective data sharing possible.
Proper citation: Open Brain Consent (RRID:SCR_022972) Copy
https://labsyspharm.github.io/jekyll-tutorial/
Website tutorial for creating Jekyll-based scientific website, including editing in GitHub, working locally with Jekyll and applying Jekyll and Markdown formatting basics, and using custom themes.
Proper citation: Jekyll Tutorial (RRID:SCR_022859) Copy
International data repository for science, engineering and design. Services include curation, sharing, long-term access and preservation of research datasets. These services are available to anyone around the world. In addition, 4TU.ResearchData also offers training and resources to researchers to support them in making research data findable, accessible, interoperable and reproducible (FAIR).
Proper citation: 4TU.ResearchData (RRID:SCR_023125) Copy
https://github.com/im3sanger/dndscv
Software R package is group of maximum likelihood dN/dS methods designed to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole-exome level.Used to detect cancer driver genes on datasets ranging from few samples to thousands of samples, in whole-exome/genome or targeted sequencing studies.
Proper citation: dNdScv (RRID:SCR_023123) Copy
https://github.com/AlexandrovLab/SigProfilerExtractor/
Software tool for de novo extraction of mutational signatures from data generated in matrix format. Identifies number of operative mutational signatures, their activities in each sample, and probability for each signature to cause specific mutation type in cancer sample.
Proper citation: SigProfilerExtractor (RRID:SCR_023121) Copy
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