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

An R / bioconductor package for detecting similarity in ordered gene lists. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.

Proper citation: OrderedList (RRID:SCR_001834) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor software package for automated gating of flow cytometry data that implements a robust model-based clustering approach based on multivariate t mixture models with the Box-Cox transformation.

Proper citation: flowClust (RRID:SCR_001807) Copy   

•   Source: SciCrunch Registry

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

Software for combinatorial polyfunctionality analysis of single cells. It is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. It uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.

Proper citation: COMPASS (RRID:SCR_001801) Copy   

•   Source: SciCrunch Registry

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

Software that provides utilities for flow cytometry data.

Proper citation: flowUtils (RRID:SCR_001879) Copy   

•   Source: SciCrunch Registry

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

Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations.

Proper citation: flowTrans (RRID:SCR_002093) Copy   

•   Source: SciCrunch Registry

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

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://sobekrepository.org/

Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories.

Proper citation: SobekCM (RRID:SCR_003225) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gemi/

Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences.

Proper citation: Gemi (RRID:SCR_003211) Copy   

•   Source: SciCrunch Registry

http://www.plexon.com/products/map-software

A suite of client / server programs that control spike sorting in the Multichannel Acquisition Processor (MAP) Data Acquisition System (MAP System) and provides real-time data visualization and analysis. Plexon's original program supporting multichannel data acquisition is a suite of programs referred to as the Real-Time Acquisition System Programs for Unit Timing in Neuroscience software (RASPUTIN). This combination of software and hardware enables users to view waveforms, acquire action potential waveforms around a voltage-threshold crossing, sort them in real time according to their shape, record continuous analog signals, such as field potentials, eye position, blood pressure, as well as capture external digital-event data, such as individual TTL lines or multi-bit strobed word data. RASPUTIN utilizes a client/server architecture on a Microsoft Windows operating system. The server program runs the MAP box and distributes the data among a set of cooperating client programs. The program can record analog signals and spike and digital-event data in a single data file, and supports 16, 32, 48, 64, 96 and 128 channel configurations. RASPUTIN's operation is based on two primary programs: Sort Client and MAP Server. The Sort Client is the primary control program for the MAP System hardware and may be used to adjust the MAP operating parameters (e.g., amplification, filtering) and to set the specific sorting parameters for each channel. MAP Server is the low-level interface for configuring the MAP, which transfers commands such as gain and filter changes or parameter settings from the various clients to the MAP box. MAP Server also accumulates data coming from the MAP box in a circular buffer memory. The client programs connect to MAP Server to gain access to that data. MAP Server also mediates communication between the clients, keeping them informed of commands sent to the MAP from other clients. RASPUTIN is not sold separately, but rather arrives pre-loaded on the MAP Control Computer with the purchase of any MAP System. As the MAP System has been replaced by the advanced OmniPlex D Neural Data Acquisition System, Plexon is no longer developing the RASPUTIN software program.

Proper citation: MAP Software (RRID:SCR_003170) Copy   

•   Source: SciCrunch Registry

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

Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

Proper citation: QDNAseq (RRID:SCR_003174) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/amplicon/

Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac

Proper citation: Amplicon (RRID:SCR_003294) Copy   

•   Source: SciCrunch Registry