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https://github.com/raamana/neuropredict

Software tool for assessment of predictive power, with support for neuroimaging features. Easy machine learning and standardized predictive analysis of biomarkers.

Proper citation: neuropredict (RRID:SCR_017405) Copy   

•   Source: SciCrunch Registry

https://www.liebertpub.com/doi/pdf/10.1089/15279160150518540

Software package for statistical analysis by SAS Institute Inc, Cary, NC.

Proper citation: StatView Version 5.0 (RRID:SCR_017411) Copy   

•   Source: SciCrunch Registry

https://usegalaxy.eu

Software tool for analysis of mass spectrometry imaging data implemented in Galaxy framework. Provides options to analyze mass spectrometry imaging data in imzML file format, including quality control, visualization, preprocessing, statistical analysis, image co-registration and feature identification.Galaxy docker container for mass spectrometry imaging.

Proper citation: Mass spectrometry imaging workbench (RRID:SCR_017410) Copy   

•   Source: SciCrunch Registry

http://carolina.imis.athena-innovation.gr/mirextra/

Software tool for analysis of expression data for microRNA function.

Proper citation: DIANA-mirExTra (RRID:SCR_017498) Copy   

•   Source: SciCrunch Registry

https://umgear.org/

Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data.

Proper citation: gene Expression Analysis Resource (RRID:SCR_017467) Copy   

•   Source: SciCrunch Registry

http://qutublab.rice.edu/cytoNet/

Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory.

Proper citation: cytoNet (RRID:SCR_017465) Copy   

•   Source: SciCrunch Registry

https://anvilproject.org/

Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces.

Proper citation: Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) Copy   

•   Source: SciCrunch Registry

http://neurocics.udd.cl/LANtoolbox.html

Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB.

Proper citation: LAN toolbox (RRID:SCR_017629) Copy   

•   Source: SciCrunch Registry

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

Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method.

Proper citation: Mediation Analysis of Causality under Confounding (RRID:SCR_017442) Copy   

•   Source: SciCrunch Registry

https://github.com/gdancik/shinyGEO

Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets.

Proper citation: shinyGEO (RRID:SCR_017605) Copy   

•   Source: SciCrunch Registry

https://github.com/Mark-Kramer/Seizure-Waves

Analysis and modeling code for waves of seizure activity.

Proper citation: Seizure-Waves (RRID:SCR_017455) Copy   

•   Source: SciCrunch Registry

http://www.mysamplesize.com

Software tool for experimental design, sample size determination and analysis by Tempest Technologies.

Proper citation: mysamplesize (RRID:SCR_017575) Copy   

•   Source: SciCrunch Registry

http://refgenie.databio.org

Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis.

Proper citation: refgenie (RRID:SCR_017574) Copy   

•   Source: SciCrunch Registry

https://leora-software.com/products/poloplusonline

Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB.

Proper citation: PoloPlus USB Drive software (RRID:SCR_017614) Copy   

•   Source: SciCrunch Registry

http://statpackets.org/

Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together.

Proper citation: StatPackets (RRID:SCR_017613) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/rjags/index.html

Software package provides interface from R to JAGS library for Bayesian data analysis. Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.

Proper citation: rjags (RRID:SCR_017573) Copy   

•   Source: SciCrunch Registry

https://github.com/padster/pyDynamo/

Software tool for neuron timelapse reconstruction, registration and analysis for Dynamic Morphometrics.

Proper citation: Dynamo (RRID:SCR_017541) Copy   

•   Source: SciCrunch Registry

https://github.com/LaBiOS/Transcriptive

Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results.

Proper citation: Transcriptive (RRID:SCR_017545) Copy   

•   Source: SciCrunch Registry

https://www.qiagenbioinformatics.com/products/clc-genomics-server/

Commercially available software tool for high throughput sequencing analysis, designed for use on central compute cluster or server. Can handle data volumes beyond capacity of desktop systems and manages submission of many jobs via its own queuing system or through submission of jobs to third party grid scheduler.

Proper citation: CLC Genomics Server (RRID:SCR_017396) Copy   

•   Source: SciCrunch Registry

http://paintmychromosomes.com/

Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data.

Proper citation: fineSTRUCTURE (RRID:SCR_018170) Copy   

•   Source: SciCrunch Registry