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https://uk.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image

Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform.

Proper citation: Tools for NIfTI and ANALYZE image (RRID:SCR_016895) Copy   

•   Source: SciCrunch Registry

https://github.com/SofieVG/FlowSOM

Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise.

Proper citation: FlowSOM (RRID:SCR_016899) Copy   

•   Source: SciCrunch Registry

https://github.com/gelles-brandeis/CoSMoS_Analysis

Software tools for analyzing co-localization single-molecule spectroscopy image data.

Proper citation: CoSMoS_Analysis (RRID:SCR_016896) Copy   

•   Source: SciCrunch Registry

https://github.com/ICB-DCM/PESTO

Software customizable toolbox for parameter estimation in MathWorks MATLAB. Offers scalable algorithms for optimization, uncertainty and identifiability analysis which do not depend on any problem-specific assumptions.

Proper citation: PESTO (RRID:SCR_016891) Copy   

•   Source: SciCrunch Registry

https://github.com/qiicr/dcmqi

Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.

Proper citation: dcmqi (RRID:SCR_016933) Copy   

•   Source: SciCrunch Registry

https://www.wizardmac.com

Software tool for data analysis and exploration. Statistics software for Mac.

Proper citation: Wizard (RRID:SCR_016939) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/neurolucida360

Software for automatic neuron 3D reconstruction and analysis. Used by neuroscientists to reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines and putative synapses.

Proper citation: Neurolucida 360 (RRID:SCR_016788) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/life-science/cell-analysis/cellular-imaging/high-content-screening/high-content-screening-instruments/hcs-studio-2.html

Software packages for quantitative cell analysis. Used in image cytometry, quantitative cell analysis or automated cell analysis in biological research and drug discovery.

Proper citation: HCS Studio Cell Analysis software (RRID:SCR_016787) Copy   

•   Source: SciCrunch Registry

https://www.networkanalyst.ca/

Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data.

Proper citation: NetworkAnalyst (RRID:SCR_016909) Copy   

•   Source: SciCrunch Registry

http://nrtdp.northwestern.edu/

Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists.

Proper citation: National Resource for Translational and Developmental Proteomics (RRID:SCR_016907) Copy   

•   Source: SciCrunch Registry

http://neuromorphometrics.com

Neuromorphometrics provides brain labeling and measurement services. Given raw MRI brain scans, we make precise quantitative measurements of the volume, shape, and location of specific neuroanatomical structures. Web tool for brain measurement services. Used for modeling living human brain and make quantitative measurements of volume, shape, and location of specific neuroanatomical structures using given MRI brain scans. Automated analyses are manually guided, inspected and certified by a neuroanatomical expert. Resource of neuroanatomically labeled MRI brain scans database. Resource for neuroanatomical localization and identification: NeuAtlas.

Proper citation: Neuromorphometrics (RRID:SCR_005656) Copy   

•   Source: SciCrunch Registry

http://thea.unice.fr/index-en.html

THIS RESOURCE IS NO LONGER IN SERVICE, on documented July 16, 2012. An integrated information processing system dedicated to the analysis of post-genomic data. It allows automatic annotation of data issued from classification systems with selected biological information (including the Gene Ontology). Users can either manually search and browse through these annotations, or automatically generate meaningful generalizations according to statistical criteria (data mining). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: THEA - Tools for High-throughput Experiments Analysis (RRID:SCR_005802) Copy   

•   Source: SciCrunch Registry

http://vortex.cs.wayne.edu/projects.htm#Onto-Express

The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially regulated in the condition under study. Independently of the methods used to select these genes, the common task faced by any researcher is to translate these lists of genes into a better understanding of the biological phenomena involved. Currently, this is done through a tedious combination of searches through the literature and a number of public databases. We developed Onto-Express (OE) as a novel tool able to automatically translate such lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. We demonstrated the validity and the utility of this comprehensive global analysis of gene function by analyzing two breast cancer data sets from two separate laboratories. OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms (Draghici et.al, Genomics, 81(2), 2003). Other results obtained with Onto-Express can be found in Khatri et.al., Genomics. 79(2), 2002. Custom level of abstraction of the Gene Ontology. User account required. Platform: Online tool

Proper citation: Onto-Express (RRID:SCR_005670) Copy   

•   Source: SciCrunch Registry

http://www.clipz.unibas.ch/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets.

Proper citation: CLIPZ (RRID:SCR_005755) Copy   

•   Source: SciCrunch Registry

http://perso.telecom-paristech.fr/~cardoso/guidesepsou.html

Blind Source Separation and Independent Component Analysis (ICA) algorithms including: An efficient batch algorithm: JADE and Adaptive algorithms: relative gradient algorithms. Associated papers / documentation are included as well as thoughts on Multi-dimensional independent component analysis. * An efficient batch algorithm: JADE - For off-line ICA, an algorithm has been developed based on the (joint) diagonalization of cumulant matrices. "Good" statistical performance is achieved by involving all the cumulants of order 2 and 4 while a fast optimization is obtained by the device of joint diagonalization. JADE has been successfully applied to the processing of real data sets, such as found in mobile telephony and in airport radar as well as to bio-medical signals (ECG, EEG, multi-electrode neural recordings). The strongest point of JADE for applications of ICA is that it works off-the-shelf (no parameter tuning). They advocate using the code provided as a plug-in replacement for PCA (whenever one is willing to investigate if such a replacement is appropriate). The weakest point of the current implementation is that the number of sources (but not of sensors) is limited in practice (by the available memory) to something like 40 or 50 depending on your computer. The JADE algorithm was originally developed to process complex signals, motivated by applications to digital communications. Another implementation is now available which is tuned to process more efficiently real-valued signals. * Adaptive algorithms: relative gradient algorithms - For adaptive source separation, they have developed a class of equivariant algorithms. This means that their performance is independent of the mixing matrix. They are obtained as stochastic relative gradient algorithms. * Multi-dimensional independent component analysis - Performing ICA on ECG signals with the JADE algorithm, it was realized that an interesting extension of the notion of independent component analysis would be to consider an analysis into linear components that would be "as independent as possible" as in ICA, but would be "livin" in subspaces of dimension greater than 1. This could be called "MICA" for Multi-dimensional Independent Component Analysis.

Proper citation: Blind Source Separation and Independent Component Analysis (RRID:SCR_002812) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.graphpad.com/

Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.

Proper citation: GraphPad Prism (RRID:SCR_002798) Copy   

•   Source: SciCrunch Registry

http://camera.calit2.net/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.

Proper citation: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) Copy   

•   Source: SciCrunch Registry

https://github.com/UCSFBiomagneticImagingLab/nutmeg

Software MEG/EEG analysis toolbox for reconstructing neural activation and overlaying it onto structural MR images. Toolbox runs under MATLAB in conjunction with SPM2 and can be used with Linux/UNIX, Mac OS X, and Windows platforms.

Proper citation: NUTMEG (RRID:SCR_002748) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview

A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.

Proper citation: Haploview (RRID:SCR_003076) Copy   

•   Source: SciCrunch Registry

http://rana.lbl.gov/drosophila

A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org.

Proper citation: Assembly/Alignment/Annotation of 12 Related Drosophila Species (RRID:SCR_002921) Copy   

•   Source: SciCrunch Registry