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http://coreimmunology.ucsf.edu/flow-cytometry

Flow cytometry facility offering training and services including:Access to two, 17-color BD LSR II analytical instruments with High Throughput Sampler (HTS) module,Configurations:LSRII 1,LSRII 2;Help with Flow Cytometry Panel Design;Fluorofinder (access our cytometers under CFAR Immunology Core);BD Panel designer;SFGH LSRII Flow Core Protocols;LSRII Startup and Shutdown;How to run the CST calibration assay;Access to a 17-color BD FACSAria II for fluorescence-activated cell sorting (FACS);4-way tube sorting;96 well plate sorting;Index sorting;SFGH ARIA Flow Core Protocols and configuration;ARIA Startup;Determining Drop Delay;Side Stream Set Up;Clog Procedure;ARIA Shutdown Protocol;ARIA Configuration;DNA analysis with standard dyes;Analysis of CFP, GFP, YFP, mRFP, mTomato, and mCherry gene expression proteins;Calcium flux measurements using Indo-1;Training of users on the operation of instruments and experimental design through the CIL Flow Cytometry Course;Maintaining and Upgrading Instruments;Research Support Services (study design, assay selection, grant and paper writing support).

Proper citation: University of California at San Francisco Division of Experimental Medicine Flow Core Facility (RRID:SCR_017903) Copy   

•   Source: SciCrunch Registry

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

A DICOM image converter based on the ITK IO mechanism for reading and writing images. The formats currently supported by the converter are DICOM to: Analyze (*.hdr); MetaImage (*.mhd); Nrrd (*.nhdr, *.nrrd).

Proper citation: DICOMConvert (RRID:SCR_014100) Copy   

•   Source: SciCrunch Registry

https://cibersort.stanford.edu/

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

Proper citation: CIBERSORT (RRID:SCR_016955) 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

http://imed.med.ucm.es/epimhc/

Database of naturally processed MHC-restricted peptide ligands and epitopes for customized computational vaccinology.

Proper citation: EPIMHC (RRID:SCR_016279) Copy   

•   Source: SciCrunch Registry

https://dbaasp.org

Collection of manually curated data regarding structure and antimicrobial activity of natural and synthetic peptides. Provides the information and analytical resources to develop antimicrobial compounds with the high therapeutic index.

Proper citation: Database of Antimicrobial Activity and Structure of Peptides (RRID:SCR_016600) Copy   

•   Source: SciCrunch Registry

https://www.immgen.org/

Project combines immunology and computational biology laboratories in effort to establish complete road map of gene-expression and regulatory networks in all immune cells. Project will generate, with rigorously standardized conditions, complete compendium of genome-wide data sets showing expression of protein-coding genes for all defined cell populations of mouse immune system.

Proper citation: ImmGen (RRID:SCR_021792) Copy   

•   Source: SciCrunch Registry

https://github.com/dviraran/xCell

Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis.

Proper citation: xCell (RRID:SCR_026446) Copy   

•   Source: SciCrunch Registry

https://github.com/GreenleafLab/chromVAR

Software R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. Enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility. Used for analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data.

Proper citation: chromvar (RRID:SCR_026570) Copy   

•   Source: SciCrunch Registry

https://github.com/RGLab/CytoML

Software R package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R.

Proper citation: CytoML (RRID:SCR_027485) Copy   

•   Source: SciCrunch Registry

https://github.com/VincentGardeux/demuxlet?tab=readme-ov-file

Software tool that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). Genetic multiplexing of barcoded single cell RNA-seq.

Proper citation: demuxlet (RRID:SCR_027855) Copy   

•   Source: SciCrunch Registry

https://github.com/zfyuan/EpiProfile2.0_Family

Software tool for processing Epi-Proteomics mass spectrometry data. Discriminates isobaric histone peptides using distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. EpiProfile 2.0 is extended version of v1.0 for enhanced quantification of histone peptides based on LC-MS/MS analysis.

Proper citation: EpiProfile (RRID:SCR_028224) Copy   

•   Source: SciCrunch Registry

https://github.com/immunogenomics/starCAT

Software pipeline that improves T cell characterization by simultaneously quantifying predefined gene expression programs (scRNA-Seq) capturing activation states and cellular subsets. Used to score cells based on a fixed, multidataset catalog of Gene Expression Programs from any tissues or cell-type.

Proper citation: starCAT (RRID:SCR_028475) Copy   

•   Source: SciCrunch Registry

https://tritrypdb.org/tritrypdb/app

Free online resource for data mining of genomic and functional data from these kinetoplastid parasites and is part of the VEuPathDB Bioinformatics Resource Center. Integrates functional genome scale datasets (e.g. transcript expression, protein expression, genetic variation data) and information predicted from automated bioinformatics pipelines and from manual curation. Provides a user friendly web interface and a number of tools and functions for users to conduct in silico experiments to ask questions and generate hypotheses. Researchers can also contribute their expertise via the User Comments form and Apollo annotation platform, and utilize cloud-based workspace to analyze their own data.

Proper citation: TryTripDB (RRID:SCR_028607) Copy   

•   Source: SciCrunch Registry