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https://github.com/PyWavelets/pywt

Software Python package for wavelet analysis.

Proper citation: PyWavelets (RRID:SCR_024421) Copy   

•   Source: SciCrunch Registry
  

https://remnrem.net/

Web Luna based interactive viewer for EDF signal and annotations, specifically designed for polysomnographic data. Supports visualization, analyses and manipulation of sleep signals, range of summary statistics and hypnogram based analyses including automated staging.

Proper citation: Moonlight (RRID:SCR_024542) Copy   

•   Source: SciCrunch Registry
  

https://sciex.com/products/software/proteinpilot-software

Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems.

Proper citation: ProteinPilot (RRID:SCR_024414) Copy   

•   Source: SciCrunch Registry
  

https://www.leicabiosystems.com/de-de/histologiegeraete/gewebeinfiltration/leica-tp1020/

Leica TP1020 tissue processor is available in four configurations: basic instrument, basic instrument with vacuum, basic instrument with fume control system and basic instrument with both vacuum and fume control. Used for gentle specimen processing and high level of specimen safety at all stages of processing run.

Proper citation: Leica: TP1020 Automatic Benchtop Tissue Processor Semi Enclosed (RRID:SCR_024535) Copy   

•   Source: SciCrunch Registry
  

https://github.com/paulgeeleher/pRRophetic

Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data,

Proper citation: pRRophetic (RRID:SCR_024417) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Martinsos/edlib

Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance.

Proper citation: Edlib (RRID:SCR_024078) Copy   

•   Source: SciCrunch Registry
  

https://qtlreaper.sourceforge.net/

Software, written in C and compiled as Python module, for rapidly scanning microarray expression data for Quantitative Trait Locies. Searches for association between each expression trait and all genotypes and evaluates that association by permutation test. Performs bootstrap resampling to estimate confidence region for location of putative QTL.

Proper citation: qtlreaper (RRID:SCR_024199) Copy   

•   Source: SciCrunch Registry
  

https://webprotege.stanford.edu

Web based platform for editing biomedical ontologies. Web application for editing OWL 2 ontologies. Open source, lightweight, web based ontology editor implemented in Java and JavaScript using OWL API and Google Web Toolkit. For users who do not wish to host their ontologies on Stanford servers, WebProtégé is available as Web app that can be run locally using Servlet container such as Tomcat.

Proper citation: WebProtege (RRID:SCR_024627) Copy   

•   Source: SciCrunch Registry
  

https://www.sdsc.edu/services/hpc/tscc/index.html

Provides advanced computing resources and services to support needs of UC San Diego research community. In addition, researchers from other academic institutions and industries can also participate in this research computing program. TSCC operates on two different computing models – Condo (a system purchase model) and Hotel (a pay-as-you-go model) to support broad range of research computing workloads including traditional HPC, HTC, and emerging big data pipelines.

Proper citation: Triton Shared Computing Cluster (RRID:SCR_024640) Copy   

•   Source: SciCrunch Registry
  

https://github.com/chaoszhang/A-pro

Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy.

Proper citation: ASTRAL-Pro (RRID:SCR_024520) Copy   

•   Source: SciCrunch Registry
  

https://p2sl.berkeley.edu/about/

Research institute dedicated to developing and deploying knowledge and tools for project management. Projects are temporary production systems. Dedicated to developing and deploying knowledge and tools for management of project production systems and the management of organizations that produce and deliver goods and services through such systems.

Proper citation: Project Production Systems Laboratory (RRID:SCR_024641) Copy   

•   Source: SciCrunch Registry
  

https://kmplot.com/analysis/

Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma.

Proper citation: Kaplan Meier Plotter (RRID:SCR_024521) Copy   

•   Source: SciCrunch Registry
  

http://madoka.denglab.org/

Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library.

Proper citation: MADOKA (RRID:SCR_024522) Copy   

•   Source: SciCrunch Registry
  

https://mia.sourceforge.net/

Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality.

Proper citation: MIA (RRID:SCR_024081) Copy   

•   Source: SciCrunch Registry
  

https://www.piscoweb.org/

Academic consortium that conducts research to advance understanding of the coastal ocean within the California Current Large Marine Ecosystem and inform management and policy.

Proper citation: Partnership for Interdisciplinary Studies of Coastal Oceans (RRID:SCR_024637) Copy   

•   Source: SciCrunch Registry
  

https://www.eneuro.org/content/10/5/ENEURO.0127-22.2023

Open source, adaptable tracking system for multiple rodents. Scalable and customizable system for tracking and behavior assessment consists of Raspberry Pi based video and RFID acquisition. Maximum of six rodents of any coat color can be tracked simultaneously in any user defined arena with few restrictions. For pose estimation and travel trajectory analysis, PyMouseTracks supports interfacing with open source packages such as DeepLabCut and Traja.

Proper citation: PyMouseTracks (RRID:SCR_024453) Copy   

•   Source: SciCrunch Registry
  

http://datamares.org

Open source, and interactive platform to resolve trans disciplinary problems related to coastal and marine ecosystem. Data sharing and science communication portal holds amounts of fishery, reef, and mangrove data pertaining to Gulf of California and Mexico specific oceans, and delivers this information in interactive and easily digestible manner. Consistently expands library of datasets while improving functionality and overall usability of the platform. Facilitate access to scientific knowledge and data to promote transparency, education, and deeper understanding of Mexico’s ecosystems and their biodiversity to bridge gap between science and design process of conservation and resource management programs.

Proper citation: DataMares (RRID:SCR_024575) Copy   

•   Source: SciCrunch Registry
  

https://www.ambulatory-monitoring.com/pvt-192-psychomotor-vigilance-monitor

System includes PVT-192 monitor and REACT software. Used for reaction time testing for long-term, large-scale testing of vigilance, effects of sleep deprivation, and drug effects. Used for PVT test wherever measures of performance or sleepiness effects are needed.

Proper citation: Ambulatory Monitoring: Psychomotor Vigilance Task system (RRID:SCR_024213) Copy   

•   Source: SciCrunch Registry
  

https://ukoethe.github.io/vigra/

Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework.

Proper citation: VIGRA (RRID:SCR_024100) Copy   

•   Source: SciCrunch Registry
  

https://proplot.readthedocs.io/en/stable/

Software tool as succinct matplotlib wrapper for making publication quality graphics.

Proper citation: ProPlot (RRID:SCR_024584) Copy   

•   Source: SciCrunch Registry