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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://services.bio.ifi.lmu.de/ProSAS

This database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several Ensembl genomes and alternative transcripts can be analyzed on the protein structure and protein function level using the intuitive user interface of the database. Users can search based on Ensembl gene or Ensembl transcript ids, Gene descriptions, Uniprot gene names, Genes matching patterns, Swissprot/Uniprot identifiers or Affymetrix probeset ids.

Proper citation: ProSAS (RRID:SCR_007876) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/maestro

Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data.

Proper citation: Maestro (RRID:SCR_016748) 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://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://bioconductor.org/packages/release/bioc/html/lumi.html

Software that provides an integrated solution for the Illumina microarray data analysis.

Proper citation: lumi (RRID:SCR_012781) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/Ringo.html

Software package that facilitates the primary analysis of ChIP-chip data.

Proper citation: Ringo (RRID:SCR_012973) 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

http://srv00.recas.ba.infn.it/ASPicDB/

A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation.

Proper citation: ASPicDB (RRID:SCR_002102) Copy   

•   Source: SciCrunch Registry

https://www.webofscience.com/wos/woscc/advanced-search

Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database.

Proper citation: Web of Science (RRID:SCR_022706) Copy   

•   Source: SciCrunch Registry

http://Mar2008.archive.ensembl.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website).

Proper citation: Ensembl Genome Browser (RRID:SCR_013367) Copy   

•   Source: SciCrunch Registry

https://github.com/stamatak/standard-RAxML

Software program for phylogenetic analyses of large datasets under maximum likelihood.

Proper citation: RAxML (RRID:SCR_006086) Copy   

•   Source: SciCrunch Registry

http://www.microrna.org

Database of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. This website enables users to explore: * The set of genes that are potentially regulated by a particular microRNA. * The implied cooperativity of multiple microRNAs on a particular mRNA. * MicroRNA expression profiles in various mammalian tissues. The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation. The microRNA Target Detection Software, miRanda, is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: microRNA.org (RRID:SCR_006997) Copy   

•   Source: SciCrunch Registry

https://uofa.ualberta.ca/biological-sciences/-/media/science/departments/biological-sciences/mbsu/fla-5000/mulitgauge20.pdf

A software application for one-dimensional electrophoretic analysis of multi-labeled fluorophores. It was designed to analyze multi-channel fluorescence data from Fujifilm FLA-5000 and FLA-8000 scanning systems. The software also works with other scanners in the BAS/FLA series and with the LAS series.

Proper citation: Multi Gauge (RRID:SCR_014299) Copy   

•   Source: SciCrunch Registry

http://www.biochem.mpg.de/5111795/maxquant

A quantitative proteomics software package for analyzing large-scale mass-spectrometric data sets. It is a set of algorithms that include peak detection and scoring of peptides, mass calibration, database searches for protein identification, protein quantification, and provides summary statistics.

Proper citation: MaxQuant (RRID:SCR_014485) Copy   

•   Source: SciCrunch Registry

http://www.qsrinternational.com/nvivo-product

Software suite for qualitative data analysis for text-based data and higher-order forms of data. Various packages are available and are dependent on the system used and the type of data analysis needed.

Proper citation: NVivo (RRID:SCR_014802) Copy   

•   Source: SciCrunch Registry

http://fatcat.burnham.org/

Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FATCAT (RRID:SCR_014631) Copy   

•   Source: SciCrunch Registry

https://github.com/hms-dbmi/spp

R analysis and processing package for Illumina platform Chip-Seq data.

Proper citation: SPP (RRID:SCR_001790) Copy   

•   Source: SciCrunch Registry

https://www.flowjo.com/solutions/flowjo

Software for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.

Proper citation: FlowJo (RRID:SCR_008520) Copy   

•   Source: SciCrunch Registry