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http://www.blast2go.com/b2ghome
An ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: Blast2GO (RRID:SCR_005828) Copy
https://github.com/davidemms/OrthoFinder
Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format.
Proper citation: OrthoFinder (RRID:SCR_017118) Copy
https://github.com/neurostuff/NiMARE
Software Python package for coordinate and image based meta analysis of neuroimaging data.
Proper citation: NiMARE (RRID:SCR_017398) Copy
http://www.broadinstitute.org/cancer/software/genepattern
A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
Proper citation: GenePattern (RRID:SCR_003201) Copy
http://www.scienceexchange.com/facilities/macquarie-university
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Set of facilities based out of Macquarie University in New South Wales. Some facilities provide services such as proteome analysis or resources of various academic departments like engineering, biological sciences, and geography.
Proper citation: Macquarie University Labs and Facilities (RRID:SCR_000944) Copy
https://tracedrawer.com/product/tracedrawer/
Software for evaluating, comparing and presenting real-time interaction data. Used for quantification of kinetics and affinity through curve fitting, with large number of binding models to choose from. Can extract experimental information from measurement, requiring minimal user input.
Proper citation: TraceDrawer (RRID:SCR_025782) Copy
http://www.geenivaramu.ee/en/tools/gwama
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for meta analysis of whole genome association data.
Proper citation: GWAMA (RRID:SCR_006624) Copy
http://microarrays.curie.fr/publications/U900-RPPA_PLT/Normacurve/
Analysis methodology that allows simultaneous quantification and normalization of reverse phase protein array (RPPA) data.
Proper citation: NormaCurve (RRID:SCR_001995) Copy
http://genewindow.nci.nih.gov/
Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible
Proper citation: GeneWindow (RRID:SCR_008183) Copy
http://bioinf.wehi.edu.au/limma/
Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.
Proper citation: LIMMA (RRID:SCR_010943) Copy
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
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
A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation.
Proper citation: AnimalTracker (RRID:SCR_014397) Copy
http://www.ccdc.cam.ac.uk/free_services/relibase_free
Web-based system for searching and analysing protein-ligand structures in the Protein Data Bank (PDB). The database provides an easily accessible web-browser interface and clear 3D structure visualisation that allows for 3D protein-ligand interaction searches, automatic superimposition and detailed analysis of related binding sites to identify protein flexibility, ligand overlap, and conserved water positions.
Proper citation: Relibase (RRID:SCR_014888) Copy
https://sedfitsedphat.nibib.nih.gov/software/default.aspx
Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.
Proper citation: SEDFIT (RRID:SCR_018365) Copy
https://www.denovosoftware.com/?gclid=EAIaIQobChMI36rn3-Dd3AIV2ud3Ch27lw2oEAAYASAAEgLbRvD_BwE
Software tool for flow and image cytometry data analysis by De Novo Software company.
Proper citation: FCS Express (RRID:SCR_016431) Copy
https://www.genomics.agilent.com/article.jsp?pageId=2100
Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MxPro QPCR (RRID:SCR_016375) Copy
Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: dCAS (RRID:SCR_016612) Copy
Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi.
Proper citation: UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) Copy
https://github.com/tomazc/iCount
Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps.
Proper citation: iCount (RRID:SCR_016712) Copy
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