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http://purl.bioontology.org/ontology/ADW

An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.

Proper citation: Animal Natural History and Life History Ontology (RRID:SCR_010292) Copy   

•   Source: SciCrunch Registry

https://pypi.org/search/?q=EmaCalc

Software package in Python for statistical analysis of Ecological Momentary Assessment data.

Proper citation: EmaCalc (RRID:SCR_022943) Copy   

•   Source: SciCrunch Registry

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

Software tool as quality assurance workflow for Brain Imaging Data Structure compliant anatomical and functional MRI datasets. Used to extract no-reference image quality metrics from structural and functional magnetic resonance imaging data.

Proper citation: MRIQC (RRID:SCR_022942) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/NCBITAXON

Ontology that is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl.

Proper citation: NCBITaxon (RRID:SCR_000479) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/DEP/

Software R package provides integrated analysis workflow for analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment.

Proper citation: Differential Enrichment analysis of Proteomics data (RRID:SCR_023090) Copy   

•   Source: SciCrunch Registry

http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/

Web application for predicting subcellular localization of plant proteins including those with multiple sites.Top Down Strategy to Augment Power for Predicting Plant Protein Subcellular Localization.

Proper citation: Plant mPLoc (RRID:SCR_023014) Copy   

•   Source: SciCrunch Registry

https://abi-services.informatik.uni-tuebingen.de/multiloc2/webloc.cgi

Web application for integrating phylogeny and Gene Ontology terms into subcellular protein colalization prediction.Extensive high performance subcellular protein localization prediction system.

Proper citation: Multi Loc2 (RRID:SCR_023013) Copy   

•   Source: SciCrunch Registry

https://github.com/schneebergerlab/syri

SyRI compares alignments between two chromosome level assemblies and identifies synteny and structural rearrangements.

Proper citation: SyRI (RRID:SCR_023008) Copy   

•   Source: SciCrunch Registry

http://www.mricro.com

Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.

Proper citation: MRIcron (RRID:SCR_002403) Copy   

•   Source: SciCrunch Registry

https://github.com/spoonsso/dannce

Convolutional neural network that calculates 3D positions of user-defined anatomical landmarks on behaving animals from videos taken at multiple angles. Works on recorded video data from multiple cameras. Used for 3D markerless pose estimation and tracking.

Proper citation: DANNCE (RRID:SCR_023061) Copy   

•   Source: SciCrunch Registry

https://stattech.ru

Web service for statistics with automated data analysis mode.

Proper citation: StatTech (RRID:SCR_023071) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/RMassBank.html

Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Proper citation: RMassBank (RRID:SCR_002797) Copy   

•   Source: SciCrunch Registry

https://github.com/Lcornet/GENERA

Software toolbox to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes.

Proper citation: GENERA (RRID:SCR_023113) Copy   

•   Source: SciCrunch Registry

http://ohnlp.org/index.php/ICEPO

An ontology distributed in OWL format which contains comprehensive terms describing ion channel electrophysiology. Terms from related ontologies, such as Cell Physiology Ontology (CPO), Cardiac Electrophysiology Ontology (CEPO), and Unit Ontology, were integrated into ICEPO.

Proper citation: ICEPO (RRID:SCR_014359) Copy   

•   Source: SciCrunch Registry

https://www.bio-techne.com/resources/instrument-software-download-center/compass-software-simple-western

Simple Western instrument software to analyze assay data and processes results.

Proper citation: Compass for Simple Western (RRID:SCR_022930) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ggsignif

Software package to indicate if two groups are significantly different. Used to add significance brackets to ggplots.

Proper citation: ggsignif (RRID:SCR_023047) Copy   

•   Source: SciCrunch Registry

https://github.com/Genomon-Project

Software DNA and RNA sequence analysis pipeline.

Proper citation: GenomonPipeline (RRID:SCR_022989) Copy   

•   Source: SciCrunch Registry

https://github.com/nextgenusfs/funannotate

Software package for genome annotation. Built specifically for fungi, but will also work with higher eukaryotes. Used for genome prediction, annotation, and comparison.

Proper citation: funannotate (RRID:SCR_023039) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry