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http://www.readout.info

Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations.

Proper citation: Neural Decoding Toolbox (RRID:SCR_009012) Copy   

•   Source: SciCrunch Registry

http://www.cisreg.ca/

This portal leads to the numerous Wasserman Lab online software tools available for use. The following are list of active Software tools available: - ConSite: Transcription factor binding site detection using phylogenetic footprinting - dbMTN: Multiple Tissue Northern Blot Comparison Tool - Gene Set Builder: A tool for collation, curation and distribution of sets of genes - The Gene Characterization Index: a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described - JASPAR: Transcription Factor Binding Profile Database - MSCAN: Algorithm that detects clusters of transcription factor binding sites in genomic sequences - NHRscan: A computational predictor of nuclear hormone receptor binding sites - oPOSSUM: Web-based analysis of over-represented transcription factor binding sites - ORCA: Transcription factor binding site detection using phylogenetic footprinting (alternative to ConSite) - OrthoSeq: Alignment of DNA sequences - PAZAR: An open-access system for the collection and dissemination of regulatory sequence annotation - Phylofoot: Tools for phylogenetic footprinting - RAVEN: Regulatory analysis of Variation in ENhancers - SAGE2Splice: A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome - TFBS: Perl modules for transcription factor binding site detection and analysis - TFCat: TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. - TFe: An online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes - Ulysses: Protein Interactions Conserved Across Evolution

Proper citation: Wasserman Lab Online Software Tools (RRID:SCR_002892) Copy   

•   Source: SciCrunch Registry

http://andestools.sourceforge.net/

Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses.

Proper citation: ANDES (RRID:SCR_002791) Copy   

•   Source: SciCrunch Registry

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

An 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

https://github.com/PacificBiosciences/R-pbh5

Software library for accessing data in HDF5 files produced by Pacific Biosciences sequencing machines. The R package supports accessing data from: cmp.h5, bas.h5, pls.h5, and trc.h5.

Proper citation: R-pbh5 (RRID:SCR_003026) Copy   

•   Source: SciCrunch Registry

http://www.semantic-measures-library.org

Open source Java library dedicated to semantic measures computation and analysis. Tools based on the SML are also provided through the SML-Toolkit, a command line software giving access to some of the functionalities of the library. The SML and the toolkit can be used to compute semantic similarity and semantic relatedness between semantic elements (e.g. concepts, terms) or entities semantically characterized (e.g. entities defined in a semantic graph, documents annotated by concepts defined in an ontology).

Proper citation: Semantic Measures Library (RRID:SCR_001383) 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

Issue

http://www.nitrc.org/projects/plink

Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.

Proper citation: PLINK (RRID:SCR_001757) Copy   

•   Source: SciCrunch Registry

https://github.com/dgleich/matlab-bgl

A Matlab package for working with graphs that uses the Boost Graph Library to efficiently implement the graph algorithms. MatlabBGL is designed to work with large sparse graphs with hundreds of thousands of nodes.

Proper citation: matlab-bgl (RRID:SCR_006981) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/fastsemsim/home/Home/

A package that implements several semantic similarity measures. It is both a library and an end-user application, featuring an intuitive graphical user interface (GUI). It has been implemented with the aim of being fast, expandable, and easy to use. It allows the user to work with the most updated version of GO database and customizable annotation corpora. It provides a set of logically-organized classes that can be easily exploited to both integrate semantic similarity into different analysis pipelines and extend the library with new measures. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: FastSemSim (RRID:SCR_006919) Copy   

•   Source: SciCrunch Registry

http://www.cns.atr.jp/dni/en/downloads/tools-for-brain-behavior-data-sharing/

This is MATLAB library to create Neuroshare data format. You can convert your own data into Neuroshare format file.

Proper citation: Matlab Neuroshare Library (RRID:SCR_006957) Copy   

•   Source: SciCrunch Registry

http://neuroshare.sourceforge.net/index.shtml

Neuroshare aims to develop a standard for accessing neurophysiological data from any vendor's acquisition device or software. An API is defined, and vendors and communities are encouraged to provide implementations of a library of functions that can read data files collected with that vendor's instrument or software. The neuroshare.org website is a collaborative, vendor-neutral area dedicated to public domain standards and software for neurophysiology.This website is part of an SBIR program funded by the National Institute for Neural Disorders and Stroke and it is currently being administered by Bionic Technologies, LLC. The goals of the SBIR program are to (Phase I) create open library and format standards for neurophysiological experiment data and (Phase II) create a set of free, open-source software tools for low-level handling and processing of neurophysiological data. Upon completion of Phase I and II, neuroshare.org will be maintained by a yet to be determined consortium of government, academic and industry partners. The SBIR was awarded in the fall of 2001 and Phase I officially began in Dec, 2001. The detailed goals of the program are summarized below:Phase I goals :(1) Establish a working group to develop and define the API library of functions.(2) A vendor-neutral web site to facilitate the development of the standards and software and publish the completed products. This site has been dubbed Neuroshare. The home page can be found at neuroshare.sourceforge.net.(3) An open, standardized API library definition for accessing neurophysiology data files. This will allow developers to produce analysis programs that can access a variety of proprietary data formats through libraries supplied by the data format owners. The manner of support will be completely determined by the research groups and vendors that supply the libraries. The Phase I standard was created by a working group consisting of international members from industry and academia. Draft standards were published for public review and comment on the neuroshare web site and revised by the working group.The grant has been awarded as a fast-track program so that Phase II begins immediately upon completion of the Phase I milestones in June 2002. Phase II will produce :(1) A set of neuroshare-compliant API libraries for existing data formats developed in collaboration with individual equipment vendors and research groups.(2) A utility for analyzing compliant API libraries for integrity and specification conformance, as well as for error checking imported data files.(3) A set of template programs in C that are meant to be used as an example on how to create a Neuroshare API compliant library and how to call it from an application,(4) An open, standardized file format for neurophysiological experiment data. This format will provide research groups and vendors with a file format for exchanging and/or publishing neural data. The format will also be powerful enough for use as a native format for researchers or vendors that wish to support it in data acquisition hardware/software.(5) Import filters that interface neuroshare-compliant API libraries to Visual Basic, MATLAB, and LabVIEW, NeuroExplorer, and Stranger analysis environments.(6) A utility program for quick header information viewing and searching to aid the organization and management of data files in the standard and proprietary formats.(7) A data file editing program for reviewing, editing, annotating, and splicing neural data files through the neuroshare API libraries and/or standard file formats. The suite will be developed in C, optimized for speed, and will run within 32-bit Windows operating systems. The availability of source code will enable eventual ports to Unix/Linux if desired(8) An add-on for the editing program that will allow review and real-time playback of multi-modal data accessible through the API and/or standard file format. These modes will include neurophysiological signals such as spikes, local field potentials and EEG, as well as experimental signals such as kinematics, stimulation, audio, video, and imaging data.(9) C and MATLAB framework programs for detection and classification of extracellular spikes in the standard data files based on classical and user-supplied algorithms.(10) A complete MATLAB application for reading data from the standard format and performing reverse correlation analysis. This program will serve as a tutorial and modifiable template for users performing analysis in MATLAB.(11) A set of export filters for creating neurophysiological data files with the neural simulation environments NEURON, NEOSIM, GENESIS, and NSL.(12) A comprehensive documentation, and help file set for all of the developed applications.Phase II will require two years of development work and software products will be made available as they are completed. As stated above, the Phase II software products will be made available as free, open-source tools. We have not decided on a license model yet, but are currently leaning towards the GNU General Public License. Revisions and bug-fixes will be maintained through the neuroshare.org website. The mission of neuroshare.org is very focused, but the specific goal list of Phase II may evolve somewhat as software is released and user feedback is received. We very interested in public suggestions about how to improve this development effort and web site. Please direct your feedback to commentsneuroshare.org or refer to our contacts page for other addresses.BackgroundThis endeavor grew out of a meeting held at the Society for Neuroscience 2000 Annual Conference in New Orleans (agenda posted here) to discuss the development of standard data formats for neuroscience. From this meeting, it was clear that although everyone supported the idea of better data portability, many vendors present wanted a standardized API (Application Program Interface) library rather than a universal data format. Based on this meeting, we submitted an SBIR application (with letters of support from key attendants of the SFN meeting) to fund the development of a standardized API definition, data format, and a suite of open source data handling and review tools.

Proper citation: Neuroshare - Open data specifications and software for neurophysiology (RRID:SCR_000005) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/cbinifti/

An I/O library for Matlab/Octave Matlab and Octave library for reading and writing Nifti-1 files. cbiNifti is intended to be a small, self-contained library that makes minimal assumptions about what Nifti files should look like and allow users easy access to the raw data. cbiNifti handles compressed file formats for reading and writing, using Unix pipes for compression and decompression. More information and code examples at: http://www.pc.rhul.ac.uk/staff/J.Larsson/software.html

Proper citation: cbiNifti: Matlab/Octave Nifti library (RRID:SCR_000860) Copy   

•   Source: SciCrunch Registry

http://unoseq.sourceforge.net/

A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists.

Proper citation: UnoSeq (RRID:SCR_005116) Copy   

•   Source: SciCrunch Registry

https://github.com/DDTBOX/DDTBOX

Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB.

Proper citation: Decision Decoding Toolbox (RRID:SCR_015978) Copy   

•   Source: SciCrunch Registry

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

Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.

Proper citation: MetaCyto (RRID:SCR_016415) Copy   

•   Source: SciCrunch Registry

https://github.com/MRCIEU/PhenoSpD

Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool.

Proper citation: PhenoSpD (RRID:SCR_016359) Copy   

•   Source: SciCrunch Registry

https://github.com/sblanck/smagexp

Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more.

Proper citation: SMAGEXP (RRID:SCR_016360) Copy   

•   Source: SciCrunch Registry

https://github.com/mikessh/migec

Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires.

Proper citation: migec (RRID:SCR_016337) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/mica/

Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.

Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy   

•   Source: SciCrunch Registry