Tools   Select Another Resource Report Type

http://david.abcc.ncifcrf.gov/content.jsp?file=/ease/ease1.htm&type=1

Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible

Proper citation: EASE: the Expression Analysis Systematic Explorer (RRID:SCR_013361) Copy   

•   Source: SciCrunch Registry

https://github.com/JCVenterInstitute/NSForest/releases

Software tool as method that takes cluster results from single cell nuclei RNAseq experiments and generates lists of minimal markers needed to define each cell type cluster. Utilizes random forest of decision trees machine learning approach. Used to determine minimum set of marker genes whose combined expression identified cells of given type with maximum classification accuracy.

Proper citation: NS-Forest (RRID:SCR_018348) Copy   

•   Source: SciCrunch Registry

http://metagenomics.anl.gov/

An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples.

Proper citation: MG-RAST (RRID:SCR_004814) Copy   

•   Source: SciCrunch Registry

https://github.com/BioDepot/BioDepot-workflow-builder

Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results.

Proper citation: BioDepot-workflow-builder (RRID:SCR_017402) Copy   

•   Source: SciCrunch Registry

https://github.com/Cai-Lab-at-University-of-Michigan/nTracer

Software tool as plug-in for ImageJ software. Used for tracing microscopic images.

Proper citation: nTracer (RRID:SCR_023032) Copy   

•   Source: SciCrunch Registry

http://crcview.hegroup.org/

Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in.

Proper citation: CRCView (RRID:SCR_007092) Copy   

•   Source: SciCrunch Registry

https://github.com/epistasislab/hibachi

Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods.

Proper citation: Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (RRID:SCR_017140) Copy   

•   Source: SciCrunch Registry

http://sites.huji.ac.il/malaria/

Data set of metabolic pathways for the malaria parasite based on the present knowledge of parasite biochemistry and on pathways known to occur in other unicellular eukaryotes. This site extracted the pertinent information from the universal sites and presented them in an educative and informative format. The site also includes, cell-cell interactions (cytoadherence and rosetting), invasion of the erythrocyte by the parasite and transport functions. It also contains an artistic impression of the ultrastructural morphology of the interaerythrocytic cycle stages and some details about the morphology of mitochondria and the apicoplast. Most pathways are relevant to the erythrocytic phase of the parasite cycle. All maps were checked for the presence of enzyme-coding genes as they are officially annotated in the Plasmodium genome (http://plasmodb.org/). The site is constructed in a hierarchical pattern that permits logical deepening: * Grouped pathways of major chemical components or biological process ** Specific pathways or specific process *** Chemical structures of substrates and products or process **** Names of enzymes and their genes or components of process Each map is linked to other maps thus enabling to verify the origin of a substrate or the fate of a product. Clicking on the EC number that appears next to each enzyme, connects the site to BRENDA, SWISSPROT ExPASy ENZYME, PlasmoDB and to IUBMB reaction scheme. Clicking of the name of a metabolite, connects the site to KEGG thus providing its chemical structure and formula. Next to each enzyme there is a pie that depicts the stage-dependent transcription of the enzyme''s coding gene. The pie is constructed as a clock of the 48 hours of the parasite cycle, where red signifies over-transcription and green, under-transcription. Clicking on the pie links to the DeRisi/UCSF transcriptome database.

Proper citation: Malaria Parasite Metabolic Pathways (RRID:SCR_007072) Copy   

•   Source: SciCrunch Registry

http://eupathdb.org/eupathdb/

EuPathDB integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as database but unifies access to three major existing individual organism databases, PlasmoDB.org, ToxoDB.org and CryptoDB.org, and integrates these databases with data available from additional sources. Through ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases. EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with eukaryotic pathogens.

Proper citation: Eukaryotic Pathogen Database Resources (RRID:SCR_004512) Copy   

•   Source: SciCrunch Registry

http://www.usidnet.org/

Research consortium to advance scientific research in the primary immune deficiency diseases (PIDD) and: * Assemble and maintain a registry of patients with primary immunodeficiency diseases to provide a minimum estimate of the prevalence of each disorder in the United States. Provide a comprehensive clinical picture of each disorder and act as a resource for clinical and laboratory research. * Establish a multifaceted mentoring program to introduce new investigators into the field and stimulate interest and research in primary immune deficiency diseases. * Establish an advisory/review committee to maintain a cell/DNA Repository of biologic material from well-characterized PIDD patients for the advancement of scientific research USIDNET operates a large database of patient information for your use. The purpose and scope of this project is to assemble and maintain a registry of residents with primary immunodeficiency diseases. The project was started with the Registry of U.S. Residents with Chronic Granulomatous Disease. Since then, the registry has been expanded and now collects data on all primary immunodeficiency disorders. The following are just a few of the diseases housed in the registry: Chronic Granulomatous Disease, Common Variable Immunodeficiency Disease, DiGeorge Anomaly, Hyper IgM Syndrome, Leukocyte Adhesion Defect, Severe Combined Immunodeficiency Disease, Wiskott-Aldrich Syndrome, X-Linked Agammaglobulinemia Physicians who would like to register their patients or access the registry are encouraged to contact Onika Davis or Lamar Hamilton, USIDNET team, at odavis (at) primaryimmune.org, or lhamilton (at) primaryimmune.org

Proper citation: USIDNET: US Immunodeficiency Network (RRID:SCR_004672) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/software/discovar/blog/

Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.

Proper citation: Discovar assembler (RRID:SCR_016755) Copy   

•   Source: SciCrunch Registry

https://niaid.github.io/spice/

Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.

Proper citation: SPICE (RRID:SCR_016603) Copy   

•   Source: SciCrunch Registry

http://research.mssm.edu/integrative-network-biology/Software.html

Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles.

Proper citation: proMODMatcher (RRID:SCR_017219) Copy   

•   Source: SciCrunch Registry

http://mummer.sourceforge.net/

Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.

Proper citation: MUMmer (RRID:SCR_018171) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/NetMHCpan/

Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs).

Proper citation: NetMHCpan Server (RRID:SCR_018182) Copy   

•   Source: SciCrunch Registry

http://hiv-web.lanl.gov/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. HIV Sequence Database is a database of annotated HIV sequences, plus a variety of tools and information for researchers studying HIV and SIV. The main aim of this website is to provide easy access to our sequence database, alignments, and the tools and interfaces we have produced. The HIV Sequence Database focuses on five primary goals: * Collecting HIV and SIV sequence data (all sequences since 1987) * Curating and annotating this data, and making it available to the scientific community * Computer analysis of HIV and related sequences * Production of software for the analysis of (sequence) data * The data and analyses on this site and published in a yearly printed publication, the HIV sequence Compendium, which is available free of charge.

Proper citation: HIV Sequence Database (RRID:SCR_002906) Copy   

•   Source: SciCrunch Registry

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/

Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) Copy   

•   Source: SciCrunch Registry

http://www.cbil.upenn.edu/apidots/

Note: ApiDots is currently unavailable. For data on apicomplexan EST assemblies, please see EuPathDB ApiDots is a database integrating mRNA/EST sequences from numerous Apicomplexan parasites. ESTs and mRNAs were clustered and further assembled to generate consensus sequences. These consensus sequences were then subjected to database searches against protein sequences and protein domain sequences. The underlying relational structure of this database allows researchers to analyze these data and pose biologically interesting questions.

Proper citation: ApiDots (RRID:SCR_001778) Copy   

•   Source: SciCrunch Registry

http://www.hiv.lanl.gov/content/vaccine/home.html

An overview of HIV and SIV vaccine trials and their outcomes. It was developed as a tool for compilation, search and comparison of published studies on SIV, HIV and SHIV vaccine trials in nonhuman primates. We used a set of criteria to scan Pubmed for relevant studies to enter into the database. In selecting studies for entry, priority was given to recently published studies in journals generally regarded as the primary source of information pertaining to HIV and SIV vaccine research in nonhuman primates. In most cases, we give priority to challenge studies, where the animals received a live virus to measure the "efficacy" of the immunogen(s) inoculated during the course of the investigation. The HIV Sequence Database focuses on five primary goals: *Collecting HIV and SIV sequence data (all sequences since 1987) *Curating and annotating this data, and making it available to the scientific community *Computer analysis of HIV and related sequences *Production of software for the analysis of (sequence) data *Publication of the data and analyses on this site and in a yearly printed publication, the HIV sequence Compendium, which is available free of charge

Proper citation: Nonhuman Primate HIV/SIV Vaccine Trials Database (RRID:SCR_002274) Copy   

•   Source: SciCrunch Registry

http://www.hiv.lanl.gov/content/immunology/index

An annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites, plus related tools and information. The goal of this database is to provide a comprehensive listing of defined HIV epitopes. These data are also printed in the HIV Molecular Immunology compendium, which is updated yearly and provided free of charge to scientific researchers, both by online download and as a printed copy. The data included in this database are extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL (CD8+), T helper (CD4+), and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, tables and maps of all defined linear epitopes relative to the HXB2 reference proteins are provided. Alignments of CTL, helper T-cell, and antibody epitopes are available through the search interfaces. Only responses to HIV-1 and HIV-2 are included in the database.

Proper citation: HIV Molecular Immunology Database (RRID:SCR_002893) Copy   

•   Source: SciCrunch Registry