Tools   Select Another Resource Report Type

http://biologicstylus.sourceforge.net/

Biologic Stylus is Biologic Institute's Stylus simulation software suite. Programming Language: C++, Python

Proper citation: Biologic Stylus (RRID:SCR_002991) Copy   

•   Source: SciCrunch Registry

http://rnaseq-mats.sourceforge.net/

Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.

Proper citation: Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngsep/

Software whose main functionality is the variants detector, which allows to make simultaneous discovery of SNVs, small indels, and CNVs.Accurate variant calling across species and sequencing protocols.Used for analysis of DNA high throughput sequencing data.

Proper citation: NGSEP (RRID:SCR_012827) Copy   

•   Source: SciCrunch Registry

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

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

Proper citation: affy (RRID:SCR_012835) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ust.hk/BOOST.html

Software application (entry from Genetic Analysis Software) for a method for detecting gene-gene interactions. It allows examining all pairwise interactions in genome-wide case-control studies.

Proper citation: BOOST (RRID:SCR_013133) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/edgeR/

Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.

Proper citation: edgeR (RRID:SCR_012802) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/meanmachine/

This software can be used to analyze EEG data either using a graphical interface (GUI) or using Matlab scripts, which make use of the functions provided by the MeanMachine. As compared to other libraries, MeanMachine can handle even very large data sets like, for example, 256 channels recorded at 2KHz.

Proper citation: Mean Machine (RRID:SCR_013103) Copy   

•   Source: SciCrunch Registry

http://www.nibb.ac.jp/cortex/

The Cortical box method is an analytical method that standardizes the serial coronal sections of rodent cortex for quantitative analysis (details are written in the manual document). There are several tools necessary for this analysis. Currently, a program CxStand which is a core program of Cortical Box method is available for download. It standardizes a set of serial sections of rat cortex into standard rectangulars. Cortical box method was developed by Dr. Junya Hirokawa in the Yamamori Lab to map c-fos immunoreactivity in the rat cortex. This method was now applied to analyze the in situ data. From the original image, the cortical region is taken out and transformed, then normalized. You do this to a set of coronal sections of a rat cortex. Then, the cortex becomes a box. You can now slice the cortical box at desired lamina positions for layer maps. For more information, please refer to, http://www.nibb.ac.jp/brish/Gallery/corticalboxE.html. Requirements Cortical Box Method software is written in Labview and requires Labview version 7.0 (or later) and Vision development version 7.0 (or later). Labview and Vision are products of National Instruments (http://www.ni.com/ ). I confirmed (*) the Cortical box software works in the latest versions of Labview (ver.8.6) and Vision development (ver. 8.6), which can be downloaded without charge in the National Instruments web site (http://www.ni.com/ ) and can be used as evaluation softwares for 30 days. I tested the programs on PCs running the Windows family of operating systems. *A VI called image to image does not exist in Labview 8.6, please replace it into image to image 2. Programs CxStand ver 1.01 - (English, 680KB, Latest Version (2008/09/25 Update)) Standardization of a part of cortex into a rectangular. CBanalysis - construct 3D cortical box and create specific layer maps. DensityMap - Creating denisty map of staining signals. Copyright (c) 2008 Junya Hirokawa. All rights reserved. This program is free software; you can redistribute it and/or modify it.

Proper citation: Cortical Box Method: Quantitative analysis for gene expressions in rodent cortex (RRID:SCR_013387) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.psb.ugent.be/ENIGMA/

A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007

Proper citation: ENIGMA (RRID:SCR_013400) Copy   

•   Source: SciCrunch Registry

http://neuroinformatics.mitre.org/projects.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A Java-based tool for managing and sharing MRI/DTI datasets, and related subject and protocol metadata. Data entry, data access, general query, reporting, analysis, and administrative operations occur through browser-based forms. NeuroServ works with a webserver (Tomcat) and a backend database (e.g., Postgres); a schema and over 40 forms are provided in the distribution. Support for DTI includes entry of multi-orientation raw DWI files, semi-automated normalization to the B0 image and quality filtering. Planned extensions include full DTI processing through image production and data sharing using the SSC incremental visiblity model.

Proper citation: NeuroServ (RRID:SCR_013617) Copy   

•   Source: SciCrunch Registry

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

Software which aims to better estimate the neuronal activation of an individual using the results of an independent component analysis (ICA) method applied to a temporally concatenated group of functional magnetic resonance imaging (fMRI) data (i.e., Tc-GICA method). This approach employs iterative LS solutions to refine both the individual SPs and TCs with an additional a priori assumption of sparseness in the SPs (i.e., minimally overlapping SPs) based on L(1)-norm minimization.

Proper citation: Iterative dual-regression with sparse prior (RRID:SCR_014128) Copy   

•   Source: SciCrunch Registry

http://academickarma.org

A peer review management system which encourages timely and high quality peer review by using a credit system. Reviewers complete reviews using a general webform on academickarma.org, and if that review is submited to an editor within ten days, the reviewer is awarded a certain amount of points (karma credits). The author and editor both receive the review. Editors can use Academic Karma to identify specialized reviewers for future reference. A reviewer's personal profile, which includes the amount of karma credits they've received, is connected to their ORCID account and publication record for an overview of the reviewer's work.

Proper citation: Academic Karma (RRID:SCR_014017) Copy   

•   Source: SciCrunch Registry

http://www.cyana.org/wiki/index.php/Main_Page

Software for automated structure calculation of biological macromolecules on basis of conformational constraints from nuclear magnetic resonance. Program for automated NMR protein structure calculation. CYANA requires a sufficient list of assigned chemical shifts and lists of cross-peak positions and columns from 2D, 3D, or4D NOESY spectra in order to calculate the assignment of the NOESY cross-peaks and the 3D structure of the protein in solution.

Proper citation: CYANA (RRID:SCR_014229) Copy   

•   Source: SciCrunch Registry

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

An R package for descriptive (i.e., fixed-effects) multivariate analysis with singular value decomposition.

Proper citation: ExPosition Packages (RRID:SCR_014107) Copy   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/home/sparky/

A graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers. Sparky displays NMR spectra, the peaks of which users may pick, assign, and integrate using a graphical interface. Users can work with any number of 2, 3 or 4 dimensional spectra simultaneously. Spectra for input to Sparky can be produced with processing programs NMRPipe, Felix, VNMR, XWinNMR or UXNMR. Output consists of text peak lists showing assignments, chemical shifts, volumes, line widths, etc.

Proper citation: Sparky (RRID:SCR_014228) Copy   

•   Source: SciCrunch Registry

http://www.moleculardevices.com/systems/microplate-readers/softmax-pro-data-acquisition-and-analysis-software

A software package for microplate reader control and microplate data analysis. It includes analysis templates for a variety of assays run on Molecular Devices microplate readers.

Proper citation: SoftMax Pro Data Acquisition and Analysis Software (RRID:SCR_014240) Copy   

•   Source: SciCrunch Registry

http://www.cytobank.org/index.html

A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow.

Proper citation: Cytobank (RRID:SCR_014043) Copy   

•   Source: SciCrunch Registry

http://www.choosemuse.com

It is a portable scalp electroencephalography (EEG) system that can be used to measure brain activity. It is battery powered and has four active electrodes located at 10-20 coordinates TP9, AF7, AF8, and TP10, a common mode reference, and a driven right leg. It includes an accelerometer and gyroscope, and works with desktop and mobile EEG acquisition and visualization software. Muse 2 expands upon the first model with increasingly robust hardware.

Proper citation: Muse: Portable Scalp EEG Device (Muse S Athena) (RRID:SCR_014418) Copy   

•   Source: SciCrunch Registry

http://msstats.org/

A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations.

Proper citation: MSstats (RRID:SCR_014353) Copy   

•   Source: SciCrunch Registry

http://www.icpsr.umich.edu/CrimeStat/about.html

A spatial statistics program which provides tools for crime mapping and analyzing crime incident locations. CrimeStat is organized into five sections: data setup, which arranges and organizes the location data; spatial description, which performs analyses such spatial distribution, spatial autocorrelation, and distance and hot spot analysis; spatial modeling, which performs a number of analyses such as Bayesian journey to crime analysis and space-time analysis; crime travel demand modeling, which detects crime patterns and correlations over time and space; and CrimeStat libraries, which are component objects that include all of the routines that were developed through version 2.0 of the regular CrimeStat program.

Proper citation: CrimeStat (RRID:SCR_014243) Copy   

•   Source: SciCrunch Registry