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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

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

http://phenex.phenoscape.org/

Software application for annotating character matrix files with ontology terms. Character states can be annotated using Entity-Quality syntax, where entity, quality, and possibly related entities are drawn from requisite ontologies. In addition, taxa (the rows of a character matrix) can be annotated with identifiers from taxonomy ontology. Phenex saves ontology annotations alongside original free text character matrix data using new NeXML format standard for evolutionary data.

Proper citation: Phenex (RRID:SCR_021748) Copy   

•   Source: SciCrunch Registry

https://www.nanostring.com/products/ncounter-analysis-system/ncounter-systems-overview/

System includes hardware and software. Options include nCounter SPRINT,nCounter MAX or nCounter FLEX. Platform used for multiplex analysis of up to 800 RNA, DNA, or protein targets. System can be combined with GeoMx Digital Spatial Profiler (DSP) to enable high-plex, spatially-resolved RNA, and protein quantification.

Proper citation: NanoString: nCounter Analysis System (RRID:SCR_021712) Copy   

•   Source: SciCrunch Registry

https://yaml.org

YAML is a human friendly data serialization language for all programming languages. Unicode based data serialization language designed around common native data types of agile programming languages. Useful for programming needs ranging from configuration files to Internet messaging to object persistence to data auditing.

Proper citation: YAML (RRID:SCR_021710) Copy   

•   Source: SciCrunch Registry

https://www.trikinetics.com/

System from TriKinetics for monitoring Drosophila activity. Includes hardware and DAMSystem3 Software for data acquision and DAMFileScan Software for scanning data for errors. Applied to behavioral activity experiments, including sleep deprivation analyses and general studies of hypoactivity and hyperactivity.

Proper citation: TriKinetics: Drosophila Activity Monitoring System (RRID:SCR_021798) Copy   

•   Source: SciCrunch Registry

https://manualzz.com/doc/6543996/drosophila-activity-monitoring-system-user-s-guide

Software tool used in Drosophila Activity Monitor system to scann data for errors. Also allows user to extract data from monitor files and bin data in different lengths.

Proper citation: Trikinetics DAM FileScan (RRID:SCR_021817) Copy   

•   Source: SciCrunch Registry

https://www.mpi.nl/

Institute is entirely devoted to psycholinguistics – the study of how we produce and understand language, and how we acquire these skills as first or second language learners. The only institution in the world entirely dedicated to psycholinguistics, and is also one of only three among total of 90 within the Max Planck Society to be located outside Germany.

Proper citation: Max Planck Institute for Psycholinguistics; Nijmegen; Netherlands (RRID:SCR_021706) Copy   

•   Source: SciCrunch Registry

https://archive.mpi.nl/tla/elan

Software annotation tool for audio and video recordings. Annotation can be sentence, word or gloss, comment, translation or description of any feature observed in media. Annotations can be created on multiple layers. Tiers can be hierarchically interconnected. Annotation can either be time-aligned to media or it can refer to other existing annotations. Content of annotations consists of Unicode text and annotation documents are stored in XML format (EAF).

Proper citation: ELAN (RRID:SCR_021705) Copy   

•   Source: SciCrunch Registry

https://github.com/igordot/sns

Set of automated workflows for common sequencing based (Illumina) protocols, such as RNA-seq, ChIP-seq, ATAC-seq, WGBS/RRBS methylation, whole genome/exome/targeted variant detection, and contaminant screening. Sequencing data analysis pipelines.

Proper citation: Seq-N-Slide (RRID:SCR_021752) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/dries_decap/halvadeforspark/

Software implements germline and somatic variant calling pipelines based on best practices pipelines from Broad Institute using Spark framework. Produces VCF output file which contains single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) when supported by used tools. Program requires Spark on either local cluster with one or more nodes, Amazon EMR cluster or Docker image to run.

Proper citation: Halvade Somatic (RRID:SCR_021771) Copy   

•   Source: SciCrunch Registry

http://justusrandolph.net/kappa/

Software tool can be used to calculate kappa, chance adjusted measure of agreement, for any number of cases, categories, or raters.

Proper citation: Online Kappa Calculator (RRID:SCR_021770) Copy   

•   Source: SciCrunch Registry

https://www.mangold-international.com/en/products/software/behavior-research-with-mangold-interact

Software platform for synchronized viewing and analysis of video footage and audio files in observational research by Mangold International GmbH. Qualitative and quantitative video coding software.

Proper citation: Interact (RRID:SCR_019254) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=cthist

Software tool for mass downloading of historical clinical trial data from ClinicalTrials.gov.

Proper citation: cthist (RRID:SCR_019229) Copy   

•   Source: SciCrunch Registry

https://sils.fnwi.uva.nl/bcb/objectj/

Software tool used for non destructive marking and linked results in ImageJ. Integrates image analysis across many images or stacks into single project file.

Proper citation: ObjectJ (RRID:SCR_019190) Copy   

•   Source: SciCrunch Registry

https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019231.pdf

HoloMonitor live cell imaging and analysis system by Phase Holographic Imaging PHI AB. Contains small, digital live cell, quantitative phase imaging microscope HoloMonitor M4 designed to operate constantly inside incubator and HoloMonitor cell imaging software App Suite or Hstudio to continuously monitor and quantitatively analyze both individual cells and cell populations over time without any cellular labels or stains. Microscope can operate in cell incubator, hypoxia chamber or on lab bench.

Proper citation: Phase Holographic Imaging: HoloMonitor live cell imaging and analysis system (RRID:SCR_019231) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/en/products/atomic-absorption/atomic-absorption-systems/240fs-aa

Atomic Absorption System determines the concentration of all elements from a single aspiration.

Proper citation: Agilent: 240FS AA Atomic Absorption System (RRID:SCR_019397) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/en/products/ftir/ftir-compact-portable-systems/5500-series-compact-ftir

Portable FTIR analyzer from Agilent 5500 Series with compact dimentions are small-sized, mid-infrared region spectrometers designed to provide capabilities of larger, traditional FTIR systems.

Proper citation: Agilent: 5500 Series Compact FTIR (RRID:SCR_019412) Copy   

•   Source: SciCrunch Registry