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https://github.com/ahmohamed/NetPathMiner

Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths.

Proper citation: NetPathMiner (RRID:SCR_002757) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowFP.html

A Bioconductor software package for fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.

Proper citation: flowFP (RRID:SCR_001537) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.7/bioc/html/plateCore.html

Software that provides basic S4 data structures and routines for analyzing plate based flow cytometry data.

Proper citation: plateCore (RRID:SCR_001743) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowClust.html

A Bioconductor software package for automated gating of flow cytometry data that implements a robust model-based clustering approach based on multivariate t mixture models with the Box-Cox transformation.

Proper citation: flowClust (RRID:SCR_001807) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/COMPASS.html

Software for combinatorial polyfunctionality analysis of single cells. It is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. It uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.

Proper citation: COMPASS (RRID:SCR_001801) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowUtils.html

Software that provides utilities for flow cytometry data.

Proper citation: flowUtils (RRID:SCR_001879) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowTrans.html

Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations.

Proper citation: flowTrans (RRID:SCR_002093) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/GeneExpressionSignature.html

An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.

Proper citation: GeneExpressionSignature (RRID:SCR_000455) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/pbcore

Software Python library for reading and writing PacBio data files.

Proper citation: pbcore (RRID:SCR_000454) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowQ.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for flow cytometry data.

Proper citation: flowQ (RRID:SCR_000575) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/SigFuge.html

Algorithm for testing significance of clustering in RNA-seq data.

Proper citation: SigFuge (RRID:SCR_000444) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowWorkspace.html

Software package that facilitates comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

Proper citation: flowWorkspace (RRID:SCR_001155) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/chimera.html

A Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools. The current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, tophat-fusion-post and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools.

Proper citation: Chimera (RRID:SCR_002959) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/triplex.html

Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

Proper citation: Triplex (RRID:SCR_003061) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html

Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

Proper citation: QDNAseq (RRID:SCR_003174) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowBin.html

A software package to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them. It establishes common bins across tubes in terms of the common markers, then determines expression within each tube for each bin in terms of the tube-specific markers.

Proper citation: flowBin (RRID:SCR_000051) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowFlowJo.html

A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.

Proper citation: flowFlowJo (RRID:SCR_000410) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowStats.html

Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package.

Proper citation: flowStats (RRID:SCR_000399) Copy   

•   Source: SciCrunch Registry

https://www.rad.upenn.edu/sbia/software/index.html#hammer

Software package that performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements. In order to make HAMMER as robust as possible to different acquisition protocols and conditions, they provide a distribution that assumes that images have been skull-stripped and segmented into gray matter, white matter, and ventricular CSF. We have other software tools that can perform these steps, including skull stripping, reorientation and reslicing, and segmentation tools. Importantly, they use 250 for WM, 150 for GM, 50 for Ventricles and 10 for CSF in the tissue-segmented brain images. Current modules used for group analysis: Labeling subject brain using a manually-labeled brain Model; Generating RAVENS map for each tissue (WM, GM, VN); Normalizing subject brain images

Proper citation: Hierarchical Attribute Matching Mechanism for Elastic Registration (RRID:SCR_001960) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/brainvox/

An interactive 3D rendering and neuroanatomical analysis package developed for analyzing focal brain lesions and functional brain imaging data (Damasio and Frank, 1991; Frank, Damasio and Grabowski, 1997).

Proper citation: Brainvox (RRID:SCR_009448) Copy   

•   Source: SciCrunch Registry