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

Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process.

Proper citation: flowMap (RRID:SCR_002269) Copy   

•   Source: SciCrunch Registry

http://cakesomatic.sourceforge.net/

A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.

Proper citation: Cake (RRID:SCR_002133) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/matchprot/

A pairwise protein structure alignment software.

Proper citation: Matchprot (RRID:SCR_002163) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.13/bioc/html/shinyTANDEM.html

Software package that provides a GUI interface for rTANDEM, an R/Bioconductor package for MS/MS protein identification. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it will also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files.

Proper citation: shinyTANDEM (RRID:SCR_002169) Copy   

•   Source: SciCrunch Registry

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

Software for matching cell populations and building meta-clusters and templates from a collection of flow cytometry (FC) samples.

Proper citation: flowMatch (RRID:SCR_002283) Copy   

•   Source: SciCrunch Registry

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

Software that identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.

Proper citation: flowMeans (RRID:SCR_002275) Copy   

•   Source: SciCrunch Registry

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

Software package that performs aggregation of ordered lists based on the ranks using several different algorithms: Borda count, Cross-Entropy Monte Carlo algorithm, Genetic algorithm, and a brute force algorithm.

Proper citation: RankAggreg (RRID:SCR_002225) Copy   

•   Source: SciCrunch Registry

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

Software for merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework.

Proper citation: flowMerge (RRID:SCR_002224) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/2.11/bioc/html/flowPhyto.html

An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.

Proper citation: flowPhyto (RRID:SCR_002183) Copy   

•   Source: SciCrunch Registry

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

Software that implements all bioinformatics steps required for the quantitative, high-resolution analysis of DNA methylation patterns from bisulfite sequencing data.

Proper citation: BEAT (RRID:SCR_002387) Copy   

•   Source: SciCrunch Registry

https://github.com/mpyatkov/sbars

Bioinformatics tool for searching different types of long repeats in sequences comparable by size with chromosomes.

Proper citation: SBARS (RRID:SCR_002371) Copy   

•   Source: SciCrunch Registry

http://personalpages.manchester.ac.uk/staff/mathias.nilsson/software.htm

Software toolbox for processing PFG NMR diffusion data that aims to incorporate many of the important processing schemes. It has a graphical user interface to make it easy to access a variety of different processing schemes (and a command mode for more advanced options). It is written in MATLAB, but can also be obtained as free standing compiled version that does not require a MATLAB installation. The MATLAB version runs on any platform, and the compiled version is presently available for Windows, Linux, and Mac.

Proper citation: DOSY Toolbox (RRID:SCR_002409) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.

Proper citation: CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) Copy   

•   Source: SciCrunch Registry

http://droog.gs.washington.edu/polyphred/

Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.

Proper citation: PolyPhred (RRID:SCR_002337) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/isa2/

A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.

Proper citation: Iterative Signature Algorithm (RRID:SCR_002327) Copy   

•   Source: SciCrunch Registry

https://github.com/armintoepfer/haploclique

Software providing a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.

Proper citation: HaploClique (RRID:SCR_002353) Copy   

•   Source: SciCrunch Registry

http://kirchnerlab.github.io/libmgf/

A flex/bison-based C++ Mascot Generic Format (MGF) parser library.

Proper citation: libmgf (RRID:SCR_002664) Copy   

•   Source: SciCrunch Registry

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

Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

Proper citation: ExomeDepth (RRID:SCR_002663) Copy   

•   Source: SciCrunch Registry

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

Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

Proper citation: MethylAid (RRID:SCR_002659) Copy   

•   Source: SciCrunch Registry

https://github.com/AliView

Software for aligning viewing and editing dna / aminiacid sequences, intuitive, fast and leightweight. It has been designed to meet the requirements of next generation sequencing era phylogenetic datasets.

Proper citation: AliView (RRID:SCR_002780) Copy   

•   Source: SciCrunch Registry