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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
https://github.com/Mark-Kramer/Seizure-Waves
Analysis and modeling code for waves of seizure activity.
Proper citation: Seizure-Waves (RRID:SCR_017455) Copy
Software tool for experimental design, sample size determination and analysis by Tempest Technologies.
Proper citation: mysamplesize (RRID:SCR_017575) Copy
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
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
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
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
https://github.com/padster/pyDynamo/
Software tool for neuron timelapse reconstruction, registration and analysis for Dynamic Morphometrics.
Proper citation: Dynamo (RRID:SCR_017541) Copy
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
https://www.labx.com/item/molecular-devices-molecular-dynamics-storm-860-molecular/3896212
Multifunction phosphoimager fluorimager laser scanner that collects fluorescent or storage phosphor images from gels, membranes and phosphor screens. It is equipped with blue (450 nm) and red (635 nm) lasers, can scan at resolutions down to 50 microns. It is able to quantify radioactive gels for commonly used isotopes such as 32P, 33P, 125I, 35S, and 14C. There are three detection modes: phosphor screen mode, red/blue fluorescence, chemifluorescence.
Proper citation: Molecular Dynamics Storm 860 Molecular Imager (RRID:SCR_018032) Copy
https://www.rcon-ndt.com/wp-content/uploads/Nanotom.pdf
System for scientific and industrial nanofocus computed tomography nanoCT and 3D metrology. Realizes unique spatial and contrast resolution on wide sample and application range. Used in material science, precision injection moulding, micromechanics, electronics geology and biology. Used in 3D CT applications. Allows many analysis, e.g. non-destructive visualization of slices, arbitrary sectional views, or automatic pore analysis.
Proper citation: Phoenix Nanotom S (RRID:SCR_017995) Copy
https://bioconductor.org/packages/TCGAbiolinks/
Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R.
Proper citation: TCGAbiolinks (RRID:SCR_017683) Copy
https://www.mbfbioscience.com/wormlab
Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays.
Proper citation: Worm Lab (RRID:SCR_017669) Copy
Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid.
Proper citation: MOON (RRID:SCR_018005) Copy
https://www.mbfbioscience.com/help/vesselucida-explorer/Content/VesselucidaExplorer.html
Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more.
Proper citation: Vesselucida Explorer (RRID:SCR_017674) Copy
https://www.mirion.com/products/genie-2000-basic-spectroscopy-software
Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data.
Proper citation: Genie 2000 Basic (RRID:SCR_021933) Copy
A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.
Proper citation: ToppCluster (RRID:SCR_001503) Copy
https://github.com/QMICodeBase/TORTOISEV4
An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.
Proper citation: TORTOISE (RRID:SCR_001645) Copy
https://github.com/sansomlab/tenx
Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis.
Proper citation: tenx (RRID:SCR_016957) Copy
http://www.nitrc.org/projects/nutil/
Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems.
Proper citation: Nutil - Neuroimaging utilities (RRID:SCR_017183) Copy
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