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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://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://software.broadinstitute.org/morpheus/

Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis.

Proper citation: Morpheus by Broad Institute (RRID:SCR_017386) 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

https://github.com/santeripuranen/SpydrPick

Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree.

Proper citation: SpydrPick (RRID:SCR_018176) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SuperDCA

Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis.

Proper citation: SuperDCA (RRID:SCR_018175) 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://nemoanalytics.org/

Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.

Proper citation: NeMO Analytics (RRID:SCR_018164) Copy   

•   Source: SciCrunch Registry

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   

•   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

http://compbio.mit.edu/ChromHMM/

Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.

Proper citation: ChromHMM (RRID:SCR_018141) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://toppcluster.cchmc.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry