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http://www.tree-puzzle.de

Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set.

Proper citation: TREE-PUZZLE (RRID:SCR_024382) Copy   

•   Source: SciCrunch Registry

https://sciex.com/products/software/proteinpilot-software

Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems.

Proper citation: ProteinPilot (RRID:SCR_024414) Copy   

•   Source: SciCrunch Registry

https://pattern.health

Platform for researchers to economically create and manage digital health programs. Platform built for research management and digital interventions. Helps researchers collect data and engage participants.

Proper citation: Pattern Health Digital Research Platform (RRID:SCR_024468) Copy   

•   Source: SciCrunch Registry

https://www.malvernpanalytical.com/en/products/product-range/omnisec/accessories/omnisec-software

Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL.

Proper citation: OMNISEC (RRID:SCR_024485) Copy   

•   Source: SciCrunch Registry

http://pbil.univ-lyon1.fr/software/phyldog/

Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously.

Proper citation: PHYLDOG (RRID:SCR_024487) Copy   

•   Source: SciCrunch Registry

https://kmplot.com/analysis/

Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma.

Proper citation: Kaplan Meier Plotter (RRID:SCR_024521) Copy   

•   Source: SciCrunch Registry

https://www.jenoptik.com/products/cameras-and-imaging-modules/microscope-cameras/progres-usb-20-firewire/software-download-progres

Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras.

Proper citation: ProgRes Capture Pro (RRID:SCR_024489) Copy   

•   Source: SciCrunch Registry

http://madoka.denglab.org/

Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library.

Proper citation: MADOKA (RRID:SCR_024522) Copy   

•   Source: SciCrunch Registry

http://www.objectivemeasures.org/

International Symposium on Objective Measures in Auditory Implants to explore what unique measures help us to achieve the best hearing outcome for each person who needs an auditory prosthesis.

Proper citation: International Symposium on Objective Measures in Auditory Implants (RRID:SCR_003160) Copy   

•   Source: SciCrunch Registry

http://www.nationalacademies.org/nrc/

Private, non-profit institution dedicated to utilizing knowledge in science, engineering, technology and health to improve government decision making and public policy as well as increase public education and understanding. The council collects, analyzes and shares information and knowledge through activities such as consensus studies, meetings and workshops, and program and research management.

Proper citation: National Research Council (RRID:SCR_000446) Copy   

•   Source: SciCrunch Registry

https://www.piscoweb.org/

Academic consortium that conducts research to advance understanding of the coastal ocean within the California Current Large Marine Ecosystem and inform management and policy.

Proper citation: Partnership for Interdisciplinary Studies of Coastal Oceans (RRID:SCR_024637) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/gquery

Search engine for the National Library of Medicine and the National Institutes of Health. It contains databases such as PubMed, EST, and BioSystems.

Proper citation: GQuery (RRID:SCR_001455) Copy   

•   Source: SciCrunch Registry

http://rfmri.org/DPARSF

A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely.

Proper citation: DPARSF (RRID:SCR_002372) Copy   

•   Source: SciCrunch Registry

http://niftyrec.scienceontheweb.net/

Software toolbox that includes reconstruction tools for emission and transmission imaging modalities, including Single Photon Emission Computed Tomography (SPECT), Positron Emission Tomography (PET), cone-beam X-Ray CT and parallel-beam X-Ray CT. At the core of NiftyRec are efficient, GPU accelerated, projection, back-projection and iterative reconstruction algorithms. The easy to use Matlab and Python interfaces of NiftyRec enable fast prototyping and development of reconstruction algorithms. NiftyRec includes standard iterative reconstruction algorithms such as Maximum Likelihood Expectation Maximisation (MLEM), Ordered Subsets Expectation Maximisation (OSEM) and One Step Late Maximum A Posteriori Expectation Maximisation (OSL-MAPEM), for multiple imaging modalities.

Proper citation: NiftyRec (RRID:SCR_002499) Copy   

•   Source: SciCrunch Registry

http://mutdb.org/mutpredsplice/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool for identifying coding region variants which disrupt pre-mRNA splicing and the underlying mechanism.

Proper citation: MutPred Splice (RRID:SCR_000594) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/mummergpu/index.php?title=MUMmerGPU

Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer.

Proper citation: MUMmerGPU (RRID:SCR_001200) Copy   

•   Source: SciCrunch Registry

http://www.warwick.ac.uk/snpm

A toolbox for Statistical Parametric Mapping (SPM) that provides an extensible framework for voxel level non-parametric permutation/randomization tests of functional Neuroimaging experiments with independent observations. SnPM uses the General Linear Model to construct pseudo t-statistic images, which are then assessed for significance using a standard non-parametric multiple comparisons procedure based on randomization/permutation testing. It is most suitable for single subject PET/SPECT analyses, or designs with low degrees of freedom available for variance estimation. In these situations the freedom to use weighted locally pooled variance estimates, or variance smoothing, makes the non-parametric approach considerably more powerful than conventional parametric approaches, as are implemented in SPM. Further, the non-parametric approach is always valid, given only minimal assumptions. The SnPM toolbox provides an alternative to the Statistics section of SPM.

Proper citation: Statistical non-Parametric Mapping (RRID:SCR_002092) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.org/wiki/BioWiki

A meta-list that is a compilation of other biology related wikipedia pages. These listings include the wiki name, description, year of inception, pages, new pages, users, active users, new edits, and wiki logo. The table can also be downloaded in a csv formatted table.

Proper citation: BioWiki (RRID:SCR_000629) Copy   

•   Source: SciCrunch Registry

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

Matlab toolbox that implements the wavelet-based image fusion technique for orthogonal images, introduced in (Aganj et al, MRM 2012).

Proper citation: Wavelet-based Image Fusion (RRID:SCR_002007) Copy   

•   Source: SciCrunch Registry

http://www.ifti.org/

A resource for information pertaining to methodologies, tools and technologies of gene expression. The website offers resources for sequence analysis, database services, and other technologies of gene expression and regulation.

Proper citation: IFTI-Mirage (RRID:SCR_000505) Copy   

•   Source: SciCrunch Registry