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http://ceas.cbi.pku.edu.cn/index.html

Integrates many useful tools to simplify ChIP-chip analysis for biologists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CEAS (RRID:SCR_010946) Copy   

•   Source: SciCrunch Registry

http://lgsun.grc.nia.nih.gov/ANOVA/

Data analysis server / software designed to test statistical significance of gene microarray data, visualize the results, and provide links to clone information and gene index. Several public datasets are also available.

Proper citation: NIA Array Analysis (RRID:SCR_010948) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/software/minc/

A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction.

Proper citation: MINC (RRID:SCR_002391) Copy   

•   Source: SciCrunch Registry

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

Interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data. First developed on Matlab 5.3 under Linux, EEGLAB runs on Matlab v5 and higher under Linux, Unix, Windows, and Mac OS X (Matlab 7+ recommended). EEGLAB provides an interactive graphic user interface (GUI) allowing users to flexibly and interactively process their high-density EEG and other dynamic brain data using independent component analysis (ICA) and/or time/frequency analysis (TFA), as well as standard averaging methods. EEGLAB also incorporates extensive tutorial and help windows, plus a command history function that eases users'' transition from GUI-based data exploration to building and running batch or custom data analysis scripts. EEGLAB offers a wealth of methods for visualizing and modeling event-related brain dynamics, both at the level of individual EEGLAB ''datasets'' and/or across a collection of datasets brought together in an EEGLAB ''studyset.'' For experienced Matlab users, EEGLAB offers a structured programming environment for storing, accessing, measuring, manipulating and visualizing event-related EEG data. For creative research programmers and methods developers, EEGLAB offers an extensible, open-source platform through which they can share new methods with the world research community by publishing EEGLAB ''plug-in'' functions that appear automatically in the EEGLAB menu of users who download them. For example, novel EEGLAB plug-ins might be built and released to ''pick peaks'' in ERP or time/frequency results, or to perform specialized import/export, data visualization, or inverse source modeling of EEG, MEG, and/or ECOG data. EEGLAB Features * Graphic user interface * Multiformat data importing * High-density data scrolling * Defined EEG data structure * Open source plug-in facility * Interactive plotting functions * Semi-automated artifact removal * ICA & time/frequency transforms * Many advanced plug-in toolboxes * Event & channel location handling * Forward/inverse head/source modeling

Proper citation: EEGLAB (RRID:SCR_007292) Copy   

•   Source: SciCrunch Registry

http://www.usadellab.org/cms/index.php?page=trimmomatic

Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.

Proper citation: Trimmomatic (RRID:SCR_011848) Copy   

•   Source: SciCrunch Registry

http://www.gelifesciences.com/webapp/wcs/stores/servlet/catalog/en/GELifeSciences-us/products/AlternativeProductStructure_16016/29000605

Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ImageQuant (RRID:SCR_014246) Copy   

•   Source: SciCrunch Registry

https://pathcore.bsd.uchicago.edu/Downloads/HTRC_ImageScUG.pdf

Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ImageScope (RRID:SCR_014311) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/epik

Software program for pKa prediction and protonation state generation for drug like molecules.

Proper citation: Epik (RRID:SCR_016745) Copy   

•   Source: SciCrunch Registry

https://networkx.github.io/

Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

Proper citation: NetworkX (RRID:SCR_016864) Copy   

•   Source: SciCrunch Registry

https://github.com/cancerit/BRASS

Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements.

Proper citation: BRASS (RRID:SCR_017091) Copy   

•   Source: SciCrunch Registry

https://www.google.com/

American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook.

Proper citation: Google (RRID:SCR_017097) Copy   

•   Source: SciCrunch Registry

https://github.com/aldenleung/OMTools

Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles.

Proper citation: OMTools (RRID:SCR_017143) Copy   

•   Source: SciCrunch Registry

http://snf-515788.vm.okeanos.grnet.gr/

Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DIANA-mirPath (RRID:SCR_017354) Copy   

•   Source: SciCrunch Registry

http://www.scandb.org/newinterface/about.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SCAN (RRID:SCR_005185) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/mammals/haploreg/haploreg.php

HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.

Proper citation: HaploReg (RRID:SCR_006796) Copy   

•   Source: SciCrunch Registry

http://www.blender.org/

Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License. Because of the overwhelming success of the first open movie project, Ton Roosendaal, the Blender Foundation''s chairman, has established the Blender Institute. This now is the permanent office and studio to more efficiently organize the Blender Foundation goals, but especially to coordinate and facilitate Open Projects related to 3D movies, games or visual effects.

Proper citation: Blender (RRID:SCR_008606) Copy   

•   Source: SciCrunch Registry

http://scholar.google.com/

Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. Google Scholar helps you find relevant work across the world of scholarly research. Features of Google Scholar * Search diverse sources from one convenient place * Find articles, theses, books, abstracts or court opinions * Locate the complete document through your library or on the web * Learn about key scholarly literature in any area of research How are documents ranked? Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature. * Publishers - Include your publications in Google Scholar * Librarians - Help patrons discover your library''s resources

Proper citation: Google Scholar (RRID:SCR_008878) Copy   

•   Source: SciCrunch Registry

http://tcoffee.crg.cat/apps/tcoffee/do:regular

A multiple sequence alignment server which can align Protein, DNA and RNA sequences.

Proper citation: T-Coffee (RRID:SCR_011818) Copy   

•   Source: SciCrunch Registry

http://probcons.stanford.edu/

Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

Proper citation: ProbCons (RRID:SCR_011813) Copy   

•   Source: SciCrunch Registry

http://genevenn.sourceforge.net/

A web application creating Venn diagrams from two or three gene lists.

Proper citation: GeneVenn (RRID:SCR_012117) Copy   

•   Source: SciCrunch Registry