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https://github.com/zdk123/SpiecEasi

Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse.

Proper citation: SpiecEasi (RRID:SCR_022712) Copy   

•   Source: SciCrunch Registry

https://outbreak.info/

Resource to aggregate all outbreak information into single location during outbreaks of emerging diseases, such as COVID-19.

Proper citation: outbreak.info (RRID:SCR_018282) Copy   

•   Source: SciCrunch Registry

https://dice-database.org

Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis.

Proper citation: Database of Immune Cell Epigenomes (RRID:SCR_018259) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/timezone1/

Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes.

Proper citation: TimeZone (RRID:SCR_018564) Copy   

•   Source: SciCrunch Registry

https://www.epimodel.org/

Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics.

Proper citation: EpiModel (RRID:SCR_018539) Copy   

•   Source: SciCrunch Registry

http://tools.dice-database.org/GOnet/)

Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.

Proper citation: GOnet (RRID:SCR_018977) Copy   

•   Source: SciCrunch Registry

http://www.immunexpresso.org

Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions.

Proper citation: immuneXpresso (RRID:SCR_017578) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Maaslin2.html

SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features.

Proper citation: MaAsLin2 (RRID:SCR_023241) Copy   

•   Source: SciCrunch Registry

https://github.com/sokrypton/ColabFold

Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding.

Proper citation: ColabFold (RRID:SCR_025453) Copy   

•   Source: SciCrunch Registry

https://github.com/JLSteenwyk/ClipKIT

Software fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others. Multiple sequence alignment-trimming algorithm for accurate phylogenomic inference.

Proper citation: ClipKIT (RRID:SCR_026411) Copy   

•   Source: SciCrunch Registry

https://www.urmc.rochester.edu/microbiology-immunology/xenopus-laevis.aspx

A comprehensive resource specializing in the use of the amphibian Xenopus laevis (the African clawed frog) for biomedical and immunological research. Several genetically-defined inbred strains and clones are available for study. The facility also maintains and develops research tools such as transgenic animals, monoclonal antibodies, cell lines, DNA libraries, and molecular probes. XLRR includes a satellite facility devoted to study infectious diseases caused by iridovirus. Technical assistance, education, and training are also provided.

Proper citation: Xenopus laevis Research Resource for Immunobiology (XLRR) (RRID:SCR_014354) Copy   

•   Source: SciCrunch Registry

https://github.com/EpistasisLab/ReBATE

Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity .

Proper citation: ReBATE (RRID:SCR_017139) Copy   

•   Source: SciCrunch Registry

https://med.nyu.edu/research/scientific-cores-shared-resources/ion-laboratory

Electrophysiology core facility that is part of Ion Channels and Transporters in Immunity Research Program.Research area includes ion channel and transporter function and ionic signaling in immune cells.Users who are studying other cell types or organ systems are welcome.Provides assistance with experimental design, training, implementation, and data analysis.

Proper citation: New York University School of Medicine IonLab Core Facility (RRID:SCR_021754) Copy   

•   Source: SciCrunch Registry

https://github.com/ScilifelabDataCentre/node-pathogens-portal

Software package and code for Pathogen Portal node (i.e. a local Pathogens Portal, such as the Swedish and Dutch Pathogens Portals). Allows users to create their own node quickly and easily.

Proper citation: Pathogens Portal Node Toolbox (RRID:SCR_027086) Copy   

•   Source: SciCrunch Registry

https://curie.utmb.edu/prosurf.html

Web server for predicting interacting sites on protein surfaces. Analyzes solvent-accessible residues likely to participate in PPIs.Predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of protein complex.

Proper citation: InterProSurf (RRID:SCR_027791) Copy   

•   Source: SciCrunch Registry

http://www.genome.ou.edu/cneo.html

Cryptococcus neoformans is an encapsulated yeast that infects the human host via the respiratory tract where it usually causes an inapparent infection. In the susceptible host, it may disseminate, typically producing a chronic and life-threatening meningitis. The Cryptococcus neoformans serotypes A and D are responsible for the overwhelming majority of pulmonary infections in AIDS patients. Cryptococcus neoformans strain H99 Latest Data Release - May 19, 2004 To date, we have isolated ca. 3750 cDNA clones from Cryptococcus neoformans strain H99 in collaboration with Drs. Juneann Murphy and Dave Dyer at the University of Oklahoma Health Sciences Center''s Department of Microbiology and Immunology in Oklahoma City and Kent Buchanan at the Tulane University Medical School, New Orleans, LA. The Cryptococcus neoformans strain H99 EST''s have been generated by Doris Kupfer, Heather Bell, Sunkyoung So, Yuong Tang, and Jennifer Lewis at the University of Oklahoma''s Advanced Center for Genome Technology, in the Department of Chemistry and Biochemistry. We now have end sequenced all available templates (ca. 7500 reactions) from both ends of the directionally cloned inserts after excision into pBlueScript SK-. . All of our data is available from our ftp site, and we now have added the ability to perform blast searches on this data. A keyword search of a blastx search of GenBank with this data also is available but we have not yet linked this to a unigene database as the number of EST''s sequenced doesn''t warrent this yet.

Proper citation: Cryptococcus Neoformans cDNA Sequencing (RRID:SCR_008462) Copy   

•   Source: SciCrunch Registry

https://omics.pnl.gov/software/ms-gf

Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.

Proper citation: MS-GF+ (RRID:SCR_015646) Copy   

•   Source: SciCrunch Registry

https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/

Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase.

Proper citation: IBEX Knowledge Base (RRID:SCR_025296) Copy   

•   Source: SciCrunch Registry

http://cryptodb.org/cryptodb/

An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data

Proper citation: ApiDB CryptoDB (RRID:SCR_013455) Copy   

•   Source: SciCrunch Registry

http://immport.org/immport-open/public/reference/cytokineRegistry

A registry of cytokines, chemokines, and receptors generated for the purpose of collecting, integrating, and mapping between entity names and synonyms from several resources. These resources include MeSH, the Protein Ontology, EntrezGene, HGNC, MGI, UniProt and others.

Proper citation: Cytokine Registry (RRID:SCR_014368) Copy   

•   Source: SciCrunch Registry