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

Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently.

Proper citation: iBMQ (RRID:SCR_000481) Copy   

•   Source: SciCrunch Registry

http://www.ddmore.eu/simulx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8, 2025. R function for computing predictions and simulating data from both Mlxtran and PharmML models that is based on MlxCompute, the model simulation engine developed by Lixoft. MlxCompute combines the Mlxtran language interpreter with the equation solvers to compute efficiently complex systems of ordinary differential equations (ODEs) and delayed differential equations (DDEs). Simulx takes advantage of the modularity of hierarchical models for simulating different components of a model: models for population parameters, individual covariates, individual parameters and longitudinal data, including continuous, count, categorical, and time-to-event data. It is also extremely flexible for defining complex dose regimens. Simulx will be the core of the next version of the DDMoRe Clinical Trial Simulator.

Proper citation: Simulx (RRID:SCR_000486) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/foursig/

A suite of software programs for analyzing and visualizing 4C-seq data.

Proper citation: fourSig (RRID:SCR_000516) 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

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://stormo.wustl.edu/DiMO/

Software for discriminative motif optimization based on perceptron training. It takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. They use the area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner.

Proper citation: DiMO (RRID:SCR_001168) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software package developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount.

Proper citation: ExomePeak (RRID:SCR_001076) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software R package for the analysis of ChIP-chip data and Affymetrix tiling arrays. It provides functions for data import, quality assessment, and data visualization. The software provides tools for the efficient mapping of genomic sequences.

Proper citation: Starr (RRID:SCR_001071) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/software/DSGseq/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 15,2025. R software program for identifying differentially spliced genes from two groups of RNA-seq samples. It reads the count file and outputs the differences in the relative abundance of the isoforms of each gene in the annotation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DSGseq (RRID:SCR_001104) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/data/annotation/html/targetscan.Hs.eg.db.html

R software that predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA.

Proper citation: targetscan.Hs.eg.db (RRID:SCR_001068) Copy   

•   Source: SciCrunch Registry

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

R package with tools for de novo motif discovery in large-scale genomic sequence data.

Proper citation: rGADEM (RRID:SCR_001091) 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://patchwork.r-forge.r-project.org/

Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data.

Proper citation: Patchwork (RRID:SCR_000072) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/manuals.html

Manuals for R created on Debian Linux that can be downloaded as PDF files, EPUB files (for R-devel and R-patched), or directly browsed as HTML. They may differ from the manuals for Mac or Windows on platform-specific pages, but most parts will be identical for all platforms.

Proper citation: R Manuals (RRID:SCR_000036) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.

Proper citation: CorMut (RRID:SCR_000053) 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

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

An R package which contains functions for validating the results of a clustering analysis.

Proper citation: clValid (RRID:SCR_014626) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/cummeRbund/index.html

Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions.

Proper citation: CummeRbund (RRID:SCR_014568) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ggplot2/index.html

Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.

Proper citation: ggplot2 (RRID:SCR_014601) Copy   

•   Source: SciCrunch Registry