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http://wpicr.wpic.pitt.edu/WPICCompGen/blocks.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software)

Proper citation: ENTROPY BLOCKER (RRID:SCR_000123) Copy   

•   Source: SciCrunch Registry

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

Software tool for performing a per vertex statistical analysis across a population. The underlying statistical framework uses the R language.

Proper citation: BRAINSSurfaceStats (RRID:SCR_002582) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/NanoStringNorm/

Software package for normalizing, diagnostics and visualization of NanoString nCounter data. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis.

Proper citation: NanoStringNorm (RRID:SCR_003382) Copy   

•   Source: SciCrunch Registry

http://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer/

A webtool which helps in characterizing Single Nucleotide Polymorphisms (SNPs) that are located in the vicinity of an SNP of interest (start SNP). Along with the computation of the maximal Linkage Disequilibrium (LD) region around the start SNP. CandiSNPer provides additional information with respect to the molecular consequences of the SNPs and the genes located in the LD region.

Proper citation: CandiSNPer (RRID:SCR_005173) Copy   

•   Source: SciCrunch Registry

https://github.com/JinmiaoChenLab/Rphenograph

Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis.

Proper citation: Rphenograph (RRID:SCR_022603) Copy   

•   Source: SciCrunch Registry

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

Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Proper citation: RMassBank (RRID:SCR_002797) Copy   

•   Source: SciCrunch Registry

https://zeppelin.apache.org/

Web based notebook that enables data driven, interactive data analytics and collaborative documents with SQL, Scala, Python, R and more. Multi purposed web based notebook which brings data ingestion, data exploration, visualization, sharing and collaboration.

Proper citation: Apache Zeppelin (RRID:SCR_023637) Copy   

•   Source: SciCrunch Registry

http://galton.uchicago.edu/~junzhang/LAPSTRUCT.html

Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software)

Proper citation: LAPSTRUCT (RRID:SCR_007550) Copy   

•   Source: SciCrunch Registry

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

R package that takes a list of p-values resulting from the simultaneous testing of hypotheses and estimates their q-values. It is designed to measure the proportion of false positives when a test is significant. The software is capable of generating plots for visualization. It can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

Proper citation: Qvalue (RRID:SCR_001073) Copy   

•   Source: SciCrunch Registry

https://igraph.org/r/

Software R package of igraph network analysis library.

Proper citation: igraph for R (RRID:SCR_021238) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/VennDiagram/

Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.

Proper citation: VennDiagram (RRID:SCR_002414) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/muma/

Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY).

Proper citation: MUMA (RRID:SCR_002412) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/nondetects.html

Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.

Proper citation: nondetects (RRID:SCR_001702) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/a/brain.org.au/ctp/

Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: cortex (RRID:SCR_002467) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/enviPick/

Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot.

Proper citation: enviPick (RRID:SCR_003059) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/stepwise/index.html

Software application that is a stepwise approach to identifying recombination breakpoints in a sequence alignment (entry from Genetic Analysis Software)

Proper citation: R/STEPWISE (RRID:SCR_007420) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/

Software application (entry from Genetic Analysis Software)

Proper citation: R/SPECTRAL-GEM (RRID:SCR_007414) Copy   

•   Source: SciCrunch Registry

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

Software R package for model selection and multimodel inference. Used for automated model selection and model-averaging. Provides wrapper for glm and other functions, automatically generating all possible models with specified response and explanatory variables.

Proper citation: glmulti (RRID:SCR_025423) Copy   

•   Source: SciCrunch Registry

https://rpy2.github.io/

Software interface to use R from Python.

Proper citation: rpy2 (RRID:SCR_024701) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/SomaticSignatures.html

Software R package for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments.

Proper citation: SomaticSignatures (RRID:SCR_025620) Copy   

•   Source: SciCrunch Registry