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http://www.bioconductor.org/packages/2.12/bioc/html/jmosaics.html

R software that detects enriched regions of ChIP-seq data sets jointly.

Proper citation: Jmosaics (RRID:SCR_001094) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/devel/bioc/html/massiR.html

Software that predicts the sex of samples in gene expression microarray datasets.

Proper citation: massiR (RRID:SCR_001157) Copy   

•   Source: SciCrunch Registry

http://denverlab.science.oregonstate.edu/tileqc/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,10, 2021.Software providing a visually oriented tile based approach to error detection for Solexa next-gen sequencing data. It is written in R and has both qualitative and quantitative error detection features. This software was written with the idea that the researcher's visual pattern recognition is the best way to detect novel errors and contains variety of ways to visualize that data. Once a new type of error is identified the data extraction features of the program may then be used as a starting point for the programmatic detection and/or filtration of similar errors. A supplementary role of tileQC is to convert the Eland and Q-score data contained within the Solexa "*_prb.txt" and "*_eland_results.txt" text files to a more flexible database form. Once in database form, tileQC simplifies the mechanics of interacting with that data and supplements standard SQL with an expression subsitution mechanism that allows R to be easily comingled with SQL. This system requires access to a mySQL server and the R package RMySQL as well as a few standard UNIX tools (also available on Windows and Macintosh).

Proper citation: TileQC (RRID:SCR_001229) Copy   

•   Source: SciCrunch Registry

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

Software R package for analysis of case-control studies in genetic epidemiology.

Proper citation: CGEN (RRID:SCR_001251) Copy   

•   Source: SciCrunch Registry

http://med.stanford.edu/tanglab/software/saber.html

Software program suitable for genome-scale data which uses a Markov-hidden Markov model (MHMM) to estimate local ancestry. The MHMM makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single-nucleotide-polymorphism panel. One application is to perform admixture mapping without genotyping special ancestry-informative-marker panels.

Proper citation: SABER (RRID:SCR_001257) Copy   

•   Source: SciCrunch Registry

http://www.wpic.pitt.edu/wpiccompgen/GemTools/GemTools.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software tools for modeling genetic ancestry based on the single nucleotide polymorphism (SNP) information. This package of functions helps the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy. It is completely written in R and runs on any platform that supports R.

Proper citation: GemTools (RRID:SCR_001259) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.jku.at/software/farms/farms.html

Software using a model-based technique for summarizing high-density oligonucleotide array data at probe level for Affymetrix GeneChips. It is based on a factor analysis model for which a Bayesian maximum a posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise.

Proper citation: FARMS (RRID:SCR_001344) Copy   

•   Source: SciCrunch Registry

https://github.com/nolanlab/cytospade

Cytoscape plugin that provides a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm for tree-based analysis and visualization of high-dimensional cytometry data.

Proper citation: CytoSPADE (RRID:SCR_001457) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/happy/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download).

Proper citation: Happy (RRID:SCR_001395) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/OLIN.html

Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data.

Proper citation: OLIN (RRID:SCR_001304) Copy   

•   Source: SciCrunch Registry

http://neuronalarchitects.com/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. A C#.NET/C++.NET 4.0 API multi-threaded, parallel class library with CUDA kernels for EEG predictive analytics gleaned from the ModelMaker 2 application. This web service and component library offers functionality to do univariate and multivariate nonlinear time series and frequency based predictive analysis for EEG / Ecog / MEG signals for gaming applications. Neural Maestro works with both EEGLab / BCILab and eConnectome as well as other MATLAB and R packages. It enables one to build highly sophisticated neuroscience applications with little effort in Windows applications.

Proper citation: Neural Maestro (RRID:SCR_001563) Copy   

•   Source: SciCrunch Registry

http://neuronalarchitects.com/about-the-workshop.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. Statistical and biomedical informatics software studio that develops neuroscience applications and brain computer interface games. They are dedicated to the integration of medical research, neuroscience, time series analysis, computer programming, statistics, sensor technologies, graphics design, artificial intelligence and entertainment to build gaming systems for neuroscientific research and intelligent tutoring in the classroom and lab. The current focus of The Cromwell Workshop/Neuronal Architects is on theoretical neuroscience and experimental modeling of psychological and neural processes that involve attention, emotion, motivation and executive functions that are impaired by neurological diseases. The outcome of this work is to use these results in the design of multiple genre brain computer interface gaming systems that can be used in both clinical and at home settings. If you would like to explore any collaborative opportunities to use their software or enhance your existing statistical products with their .NET, Java, R and Matlab code bases, let them know.

Proper citation: The Cromwell Workshop (RRID:SCR_001588) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.4/bioc/html/rMAT.html

Software package for normalizing and analyzing tiling arrays and ChIP-chip data. It is the R-version of a MAT program.

Proper citation: rMAT (RRID:SCR_001583) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/CNVrd2.html

A software package that uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

Proper citation: CNVrd2 (RRID:SCR_001723) Copy   

•   Source: SciCrunch Registry

http://talasso.cnb.csic.es/

Tool for quantification of human miRNA-mRNA Interactions. TaLasso is also available as Matlab or R code.

Proper citation: TaLasso (RRID:SCR_001726) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.med.yale.edu/group/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R code for Bayesian modeling of paired RNA-seq experiments.

Proper citation: pairedBayes (RRID:SCR_001738) Copy   

•   Source: SciCrunch Registry

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

Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.

Proper citation: unifiedWMWqPCR (RRID:SCR_001706) Copy   

•   Source: SciCrunch Registry

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

A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

Proper citation: RSVSim (RRID:SCR_001777) Copy   

•   Source: SciCrunch Registry

http://www.genabel.org/packages/GenABEL

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits.

Proper citation: GenABEL (RRID:SCR_001842) Copy   

•   Source: SciCrunch Registry

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

Software that identifies cell population in flow cytometry data. It demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. It samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample.

Proper citation: SamSPECTRAL (RRID:SCR_001858) Copy   

•   Source: SciCrunch Registry