Tools   Select Another Resource Report Type

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

Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance.

Proper citation: DMRforPairs (RRID:SCR_005702) Copy   

•   Source: SciCrunch Registry

http://staden.sourceforge.net/

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

Proper citation: Staden Package (RRID:SCR_005629) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.

Proper citation: MIMOSA (RRID:SCR_000184) Copy   

•   Source: SciCrunch Registry

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

Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.

Proper citation: iASeq (RRID:SCR_000420) Copy   

•   Source: SciCrunch Registry

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

An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.

Proper citation: rTANDEM (RRID:SCR_000409) Copy   

•   Source: SciCrunch Registry

https://github.com/yongchao/flowPeaks

Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

Proper citation: flowPeaks (RRID:SCR_000407) Copy   

•   Source: SciCrunch Registry

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

Software that provides quality control and quality assessment tools for gated flow cytometry data.

Proper citation: QUALIFIER (RRID:SCR_000389) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/sybil/

A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.

Proper citation: sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) Copy   

•   Source: SciCrunch Registry

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

Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.

Proper citation: Rdisop (RRID:SCR_000453) Copy   

•   Source: SciCrunch Registry

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

Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.

Proper citation: FlipFlop (RRID:SCR_000625) Copy   

•   Source: SciCrunch Registry

https://github.com/akiomiyao/tif

A search program to detect insertions of transposable element from short reads of next generation sequencer.

Proper citation: Transposon Insertion Finder (RRID:SCR_001159) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/jmzml/

A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard.

Proper citation: jmzML (RRID:SCR_001119) 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://www.bioconductor.org/packages/release/bioc/html/DSS.html

Software R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

Proper citation: DSS (RRID:SCR_002754) Copy   

•   Source: SciCrunch Registry

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

A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported.

Proper citation: rBiopaxParser (RRID:SCR_002744) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/src/contrib/Archive/aCGH.Spline/

An R package for array comparative genomic hybridization (aCGH) dye bias normalization.

Proper citation: aCGH.Spline (RRID:SCR_002927) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/Basic4Cseq.html

An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

Proper citation: Basic4Cseq (RRID:SCR_002836) Copy   

•   Source: SciCrunch Registry

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

Software that provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files.

Proper citation: mzR (RRID:SCR_002856) Copy   

•   Source: SciCrunch Registry

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

Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.

Proper citation: BiGGR (RRID:SCR_002854) Copy   

•   Source: SciCrunch Registry

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

An R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation.

Proper citation: PAPi (RRID:SCR_002857) Copy   

•   Source: SciCrunch Registry