Tools   Select Another Resource Report Type

https://edspace.american.edu/openbehavior/project/tonebox-system-automated-auditory-operant-conditioning/

Project related to auditory behavioral task data collection.Provided high throughput operant conditioning in mouse homecage system was developed by University of Maryland,College Park, scientists.Automated system for training up to hundreds of mice in auditory behavioral task features custom Matlab GUI running on desktop which connects to Raspberry Pi to administer auditory stimuli from USB soundcard and collects auditory data as well as licking data from water spout with commercially available capacitive sensors. Parts list and build instructions are readily available from paper and associated GitHub repository.

Proper citation: ToneBox (RRID:SCR_021548) Copy   

•   Source: SciCrunch Registry

https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md

Software tool for accurate, fast and versatile mapping/quantification of single cell and single nucleus RNA-seq data. Used for mapping, demultiplexing and quantification for single cell RNA-seq. Comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR.

Proper citation: STARsolo (RRID:SCR_021542) Copy   

•   Source: SciCrunch Registry

https://circexplorer2.readthedocs.io/en/latest/

Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs.

Proper citation: CIRCexplorer2 (RRID:SCR_021664) Copy   

•   Source: SciCrunch Registry

https://github.com/ratcave/ratcave

Software 3D graphics python package for cognitive psychology experiments. Open source, cross platform Python library that adds 3D stimulus support to all OpenGL-based 2D Python stimulus libraries. These libraries include VisionEgg, Psychopy, Pyglet, and PyGam.

Proper citation: Ratcave (RRID:SCR_021599) Copy   

•   Source: SciCrunch Registry

https://sourcemd.toolforge.org/index_old.php

Web tool as prototype service to automatically generate Wikidata items using metadata from scholarly publications. Citation lookup tool in Wikipedia platform. Takes persistent identifier for scholarly article and processes it by importing bibliographic metadata into Wikidata items. In August 2018, it was merged with ORCIDator into single tool that allows for fully automated batch processing based on ISBN-13, DOI, ORCID iD, PubMed ID, PMCID identifiers.

Proper citation: SourceMD (RRID:SCR_021633) Copy   

•   Source: SciCrunch Registry

https://github.com/mne-tools/mne-cpp

Software tool for real time processing of electrophysiological data.

Proper citation: MNE Scan (RRID:SCR_021530) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/service.php?NetMHC-4.0

Web tool for binding prediction of peptides to MHC class I molecules. The newest version NetMHC- 4.0 is used for prediction of peptide MHC class I binding affinity using gapped sequence alignment that allows insertions and deletions in alignment.

Proper citation: NetMHC (RRID:SCR_021651) Copy   

•   Source: SciCrunch Registry

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

Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.

Proper citation: Cumulus (RRID:SCR_021644) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/jcvi/

Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

Proper citation: jcvi (RRID:SCR_021641) Copy   

•   Source: SciCrunch Registry

https://hpap.pmacs.upenn.edu/about-pancdb

Portal to make all Human Pancreas Analysis Program data available to anyone in research community and to interact with and connect scientific community. Stores clinical, molecular, cellular, immunology, imaging, and pathology data from pancreatic tissue and cell samples from organ donors with and without type 1 or type 2 diabetes.

Proper citation: PANC-DB (RRID:SCR_021860) Copy   

•   Source: SciCrunch Registry

http://imj.com.au/sgs/

Software tool as biophysical simulation model for livestock systems. It has flexible interface for setting up and running simulations with extensive graphical and data output.

Proper citation: Sustainable Grazing System Pasture Model (RRID:SCR_021854) Copy   

•   Source: SciCrunch Registry

https://www.research.va.gov/mvp/

National research program to learn how genes, lifestyle, and military exposures affect health and illness.

Proper citation: Million Veteran Program (RRID:SCR_021731) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/fuzzywuzzy/

Software pacakge that uses Levenshtein Distance to calculate differences between sequences for string matching.

Proper citation: FuzzyWuzzy (RRID:SCR_021699) Copy   

•   Source: SciCrunch Registry

https://pdf.medicalexpo.com/pdf/ge-healthcare-life-sciences/amersham-imager-600/80554-135352.html

Amersham Imager 600 is CCD camera system that produces digitial images of samples in gels or membranes in three different modes: chemiluminescence, colorimetric and fluorescent image capture. Provides imaging system to capture and analyze protein and DNA sample gels and membranes in high resolution.

Proper citation: GE: Amersham Imager 600 (RRID:SCR_021853) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/BorutaShap/

Software tool as wrapper feature selection method which combines both Boruta feature selection algorithm with shapley values.

Proper citation: BorutaShap (RRID:SCR_021696) Copy   

•   Source: SciCrunch Registry

https://lightgbm.readthedocs.io/en/latest/

Software tool as gradient boosting framework that uses tree based learning algorithms. Designed to be distributed and efficient with advantages:Faster training speed and higher efficiency;Lower memory usage;Better accuracy;Support of parallel, distributed, and GPU learning;Capable of handling large scale data.

Proper citation: LightGBM (RRID:SCR_021697) Copy   

•   Source: SciCrunch Registry

https://github.com/gfairchild/pyxDamerauLevenshtein

Software tool implements Damerau-Levenshtein (DL) edit distance algorithm for Python in Cython for high performance.

Proper citation: pyxDamerauLevenshtein (RRID:SCR_021858) Copy   

•   Source: SciCrunch Registry

http://www.paintomics.org

Web tool for integrative visualization of multiple omic datasets onto KEGG pathways. Supports integrated visualization of multiple species of different biological kingdoms and offers user possibility to request any other organism present in KEGG database.

Proper citation: PaintOmics (RRID:SCR_021859) Copy   

•   Source: SciCrunch Registry

https://www.physikinstrumente.com/en/products/motion-control-software/

Software to control positioning systems without their own macro facility.

Proper citation: PI Motion Control Software (RRID:SCR_021867) Copy   

•   Source: SciCrunch Registry

https://samplesizeshop.org

Platform for multilevel and longitudinal data.Provide researchers such as behavioral and social scientists with tools and education related to study design including Calculating power and sample size for any univariate or multivariate test for general linear multivariate model, assuming fixed predictors;Producing confidence intervals on power estimates for designs with fixed predictors;Producing power calculations for designs with single Gaussian covariate;Supporting designs with unequal group sizes, and complicated covariance structures;Creating basic power curves.

Proper citation: Sample Size Shop (RRID:SCR_021747) Copy   

•   Source: SciCrunch Registry