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https://github.com/marbl/salsa

Software tool for scaffold long read assemblies with Hi-C data.

Proper citation: SALSA (RRID:SCR_022013) Copy   

•   Source: SciCrunch Registry

https://github.com/immunogenomics/harmony

Software R package to project cells into shared embedding in which cells group by cell type rather than dataset specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. Used for integration of single cell data.

Proper citation: Harmony (RRID:SCR_022206) Copy   

•   Source: SciCrunch Registry

https://www.rdocumentation.org/packages/DGCA/versions/1.0.2

Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix.

Proper citation: Differential Gene Correlation Analysis (RRID:SCR_020964) Copy   

•   Source: SciCrunch Registry

https://rdrr.io/cran/DrInsight/src/R/drug.identification.R

Software connectivity mapping based drug repurposing tool that identifies drugs that can potentially reverse query disease phenotype or have similar functions with query drugs.

Proper citation: DrInsight (RRID:SCR_023871) Copy   

•   Source: SciCrunch Registry

http://www.genome.wisc.edu/

The E. coli Genome Project has the goal of completely sequencing the E. coli and human genomes. They began isolation of an overlapping lambda clonebank of E. coli K-12 strain MG1655. Those clones served as the starting material in our initial efforts to sequence the whole genome. Improvements in sequencing technology have since reached the point where whole-genome sequencing of microbial genomes is routine, and the human genome has in fact been completed. They initiated additional sequencing efforts, concentrating on pathogenic members of the family Enterobacteriaceae -- to which E. coli belongs. They also began a systematic functional characterization of E. coli K-12 genes and their regulation, using the whole genome sequence to address how the over 4000 genes of this organism act together to enable its survival in a wide range of environments.

Proper citation: E. coli Genome project (RRID:SCR_008139) Copy   

•   Source: SciCrunch Registry

https://www.archrproject.com/

Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing.

Proper citation: ArchR (RRID:SCR_020982) Copy   

•   Source: SciCrunch Registry

https://github.com/datatagsuite

Software suite to enable discoverability of datasets. Enables submission of metadata on datasets to DataMed. Has core set of elements, which are generic and applicable to any type of dataset, and extended set that can accommodate more specialized data types. Platform independent model developed by NIH BD2K bioCADDIE project for DataMed Data Discovery Index prototype being developed. Also available as annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex.

Proper citation: DatA Tag Suite (RRID:SCR_019236) Copy   

•   Source: SciCrunch Registry

https://github.com/JamieHeather/stitchr

Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information.

Proper citation: Stitchr (RRID:SCR_022139) 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.

Proper citation: NetMHCpan Server (RRID:SCR_018182) Copy   

•   Source: SciCrunch Registry

https://www.immport.org/home

Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology.

Proper citation: The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ap_seg_2013_nih/

A MATLAB GUI for segmenting and quantifying PET images with multi-focal and diffuse uptakes. It imports a PET image and allows the user to draw region of interests (ROIs) in 2D or 3D to roughly separate the object of interest from the background. The areas are then segmented using a PET image segmentation method based on Affinity Propagation clustering to cluster the image intensities into meaningful groups. For quantification, the Standardized Uptake Value measurements of the binary or the user defined ROI are SUVmax, SUVmean, and Volume (mm^3) and can be exported into an excel sheet.

Proper citation: NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering (RRID:SCR_014151) Copy   

•   Source: SciCrunch Registry

https://cedar.metadatacenter.org/

Web application for creating, collecting, testing, and sharing metadata. It provides templates for metadata models or structures, and is capable of testing those models quickly using real data.

Proper citation: CEDAR Workbench (RRID:SCR_016270) 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

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://github.com/wyp1125/MCScanx

Software toolkit for detection and evolutionary analysis of gene synteny and collinearity.

Proper citation: MCScanX (RRID:SCR_022067) Copy   

•   Source: SciCrunch Registry

http://www.nsrrc.missouri.edu/

Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research.

Proper citation: National Swine Resource and Research Center (RRID:SCR_006855) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/IMMDIS

Ontology generated as part of the Bioinformatics Integration Support Contract (BISC) that is based on the National Library of Medicine (NLM) Medical Subject Headings; National Cancer Institute Thesaurus; International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM); ICD-10; and other open source public databases. Specific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc.

Proper citation: Immune Disorder Ontology (RRID:SCR_010344) Copy   

•   Source: SciCrunch Registry

https://bioweb.pasteur.fr/packages/pack@Tracer@v1.6

Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more.

Proper citation: Tracer (RRID:SCR_019121) Copy   

•   Source: SciCrunch Registry

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