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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

https://github.com/ANGSD/angsd

Software tool fo analysis of next generation sequencing data. Calculates various summary statistics, and performs association mapping and population genetic analyses utilizing full information in next generation sequencing data by working directly on raw sequencing data or by using genotype likelihoods.

Proper citation: ANGSD (RRID:SCR_021865) Copy   

•   Source: SciCrunch Registry

https://evofunvm.dcsr.unil.ch/

Database of metadata and assembly quality metrics for all Arthropod assemblies on NCBI.

Proper citation: Arthropoda Assembly Assessment Catalog (RRID:SCR_021864) Copy   

•   Source: SciCrunch Registry

https://github.com/seqcode/pegr

Web service platform logging metadata for genomic samples and high throughput sequencing, manages data processing workflows, and provides quality control reporting and visualization. PEGR links people, samples, protocols, sequencing and bioinformatics computation to comply with FAIR best practices for publications and data management plans.Tracks and quality controls experiments from conception to publication ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at wet bench, while continuing to fully support reproducibility and reliability for bioinformaticians through integration with Galaxy platform.

Proper citation: Platform for Epigenomic and Genomic Research (RRID:SCR_021861) 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://trialdesign.org/

Integrated platform for designing clinical trials.

Proper citation: Trialdesign (RRID:SCR_021749) Copy   

•   Source: SciCrunch Registry

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https://github.com/gabraham/flashpca

Software tool as fast principal component analysis of large scale genome wide data. FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data. FlashPCA2 used for principal component analysis of biobank scale genotype datasets.

Proper citation: FlashPCA (RRID:SCR_021680) Copy   

•   Source: SciCrunch Registry

https://github.com/ODonoghueLab/Aquaria

Web application to help biologists use 3D structures to gain insight into protein function. Used in revealing novel insights into molecular mechanisms underlying protein function in health and disease. System for incorporating 3D structures into variant analysis.

Proper citation: Aquaria (RRID:SCR_021834) Copy   

•   Source: SciCrunch Registry