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http://bioconductor.org/packages/gage/

Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies.

Proper citation: GAGE (RRID:SCR_017067) Copy   

•   Source: SciCrunch Registry

https://github.com/ZSI-Bio/bdg-sequila

Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals.

Proper citation: SeQuiLa (RRID:SCR_017220) Copy   

•   Source: SciCrunch Registry

https://github.com/csbbcompbio/CSBB-v3.0

Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments.

Proper citation: Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) Copy   

•   Source: SciCrunch Registry

http://kim.bio.upenn.edu/software/pivot.shtml

Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows.

Proper citation: PIVOT software (RRID:SCR_017210) Copy   

•   Source: SciCrunch Registry

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://www.bio-rad.com/en-eh/product/cfx-manager-software

Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CFX Manager (RRID:SCR_017251) Copy   

•   Source: SciCrunch Registry

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

Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R.

Proper citation: ape (RRID:SCR_017343) Copy   

•   Source: SciCrunch Registry

https://github.com/zuoxinian/CCS

Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies.

Proper citation: Connectome Computation System (RRID:SCR_017342) 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/Mark-Kramer/Seizure-Waves

Analysis and modeling code for waves of seizure activity.

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

•   Source: SciCrunch Registry

https://www.drive5.com/piler/

Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats.

Proper citation: PILER (RRID:SCR_017333) Copy   

•   Source: SciCrunch Registry

http://140.120.197.173/Ecology/prod02.htm

Software tool used to conduct life table analysis focused on development of cohort or population for animal species with two sexes. Parent organization is National Chung Hsing University, Taichung, Taiwan.

Proper citation: TWOSEX-MSChart (RRID:SCR_017298) Copy   

•   Source: SciCrunch Registry

https://github.com/cwatson/braingraph/

Software R package for performing graph theory analyses of brain MRI data.

Proper citation: brainGraph (RRID:SCR_017260) 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

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

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://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