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https://github.com/Crick-CancerGenomics/ascat
Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data.
Proper citation: ascat (RRID:SCR_016868) Copy
https://github.com/aroth85/pyclone
Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing.
Proper citation: Pyclone (RRID:SCR_016873) Copy
https://github.com/kendomaniac/rCASC
Software package for reproducible classification analysis of single cell sequencing data.
Proper citation: rCASC (RRID:SCR_017005) Copy
Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility.
Proper citation: Experimental Design Assistant (RRID:SCR_017019) Copy
https://github.com/ToolsVanBox/smMIPfil
Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required.
Proper citation: smMIPfil (RRID:SCR_016892) Copy
https://github.com/nolanlab/VORTEX
Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids.
Proper citation: VORTEX (RRID:SCR_017047) Copy
https://github.com/dpeerlab/phenograph
Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.
Proper citation: Phenograph (RRID:SCR_016919) Copy
https://github.com/Frederik-D-Weber/cosleep
Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton.
Proper citation: COsleep (RRID:SCR_017053) Copy
https://github.com/Rinoahu/SwiftOrtho
Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.
Proper citation: SwiftOrtho (RRID:SCR_017122) Copy
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
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
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
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
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
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
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
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
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
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
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
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