SciCrunch

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SciCrunch
10 years ago - submitted by James Go

Brain research group affiliated with the Nanjing University of Aeronautics and Astronautics (NUAA) in China. The main research interests of iBRAIN include developing methods in machine learning, data mining, neural computation, and related areas for decoding brain functions or recognizing brain disease. Research related code and datasets can be found on the main site.

RRID-Legacy
10 years ago - submitted by David Kennedy

CLIK

Statistical method that uses previously annotated interaction data to automatically determine biologically informed statistical significance cutoffs for genome-wide screens.

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RRID-Legacy
10 years ago - by Anonymous

TeachingDemos

A portal and resource for tutorials on a variety of data analysis techniques, the use of tools such as MetaMapR, workshops on data visualization, and R code manuals.

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SciCrunch
10 years ago - submitted by Kristen Jensen

SIMCA

A company that provides data analysis software with features such as multivariate tools, data mining, process modeling and interactive graphics.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Metscape

A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.

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SciCrunch
10 years ago - submitted by Kristen Jensen

MetaP

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 5,2023. Software tool for processing in metabolomics experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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SciCrunch
10 years ago - submitted by Kristen Jensen

MetaMapR

An open-source software program for integrating enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networks and display results using data visualization techniques.

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SciCrunch
10 years ago - submitted by Kristen Jensen

MBRole

Software program for overrepresentation (enrichment) analysis of categorical annotations for a set of compounds. These categorical annotations correspond to biological and chemical information found in public databases and software. Annotations can be biological (pathways, enzyme interactions, pharmacological action) or chemical (taxonomy and chemical groups).

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SciCrunch
10 years ago - submitted by Kristen Jensen

DeviumWeb

A software suite for data wrangling, creating interactive data visualization, performing statistical analyses, cluster analyses, exploratory data analysis and visualization (such as principal component analysis), predictive modeling and biochemical pathway analysis.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Chenomx NMR Suite

A software suite for identifying and quanitfying compounds in NMR spectra. Features include a compound profiler, tools to process data, a compound builder, spin simulator and library manager. More information can be requested, and installation instructions are available on the website.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Chemical Translation Service

A translation service which contains a registry of pubicly available chemical information such as structures, chemical names, chemical synonyms, database identifiers, molecular masses, XlogP and proton-donor/acceptor data for compound-specific, structure-based cross references. It offers single ID conversion, batch ID conversion, InChI code conversion, and other services.

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SciCrunch
10 years ago - submitted by Kristen Jensen

NIST Mass Spectrometry Data Center

A data center that develops evaluated mass spectral libraries and provides related software tools that assist compound identification by providing reference mass spectra for GC/MS (by electron ionization) and LC-MS/MS (by tandem mass spectrometry). It also provides gas phase retention indices for GC. Resources include the mass spectral library, the peptide library, and a standard refernece material guide.

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SciCrunch
10 years ago - submitted by Kristen Jensen

ACD/ NMR Processor

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 27, 2016. A software package that provides 1D and 2D NMR tools as well as processing and interpretation for all other major analytical techniques (LC/MS, IR, Raman, and more) in one package. It also has support for structure verification and multiplet reports.

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SciCrunch
10 years ago - submitted by Kristen Jensen

3Omics

THIS RESOURCE IS NO LONGER IN SERVICE, documented October 19, 2016. A web tool for visualizing and integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data. 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for transcripts, proteins and metabolites.

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SciCrunch
10 years ago - submitted by Kristen Jensen

mwtabR

An R package that downloads and parses mwtab data from Metabolomics Workbench studies. Downloaded files are converted into R lists.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Principal Components Analysis

R documentation for a function that performs a principal components analysis on a given data matrix and returns the results as an object of class prcomp.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Linear Discriminant Analysis

R documentation for a function to perform linear discriminant analysis; specifically, to detect if the within-class covariance matrix is singular.

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SciCrunch
10 years ago - submitted by Kristen Jensen

imDEV

A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Hierarchical Clustering

R documentation for hierarchical cluster analysis on a set of dissimilarities for n objects. Each object is assigned to its own cluster, which an algorithm proceeds through iteratively. Two of the most similar clusters are joined at each stage until there is a single cluster. Distances between clusters are recomputed at each stage by the Lance–Williams dissimilarity update formula according to the particular clustering method being used. Clustering methods include: Ward's minimum variance method, complete linkage method, and single linkage method.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

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