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https://nemoanalytics.org/

Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.

Proper citation: NeMO Analytics (RRID:SCR_018164) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/ChromHMM/

Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.

Proper citation: ChromHMM (RRID:SCR_018141) Copy   

•   Source: SciCrunch Registry

https://biit.cs.ut.ee/gprofiler/page/r

Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool.

Proper citation: gProfiler2 (RRID:SCR_018190) Copy   

•   Source: SciCrunch Registry

http://ultrascan.aucsolutions.com/

Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis.

Proper citation: UltraScan (RRID:SCR_018126) 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

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   

•   Source: SciCrunch Registry

http://pinet-server.org

Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.

Proper citation: piNET (RRID:SCR_018693) Copy   

•   Source: SciCrunch Registry

https://cistrome.shinyapps.io/timer/

Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features.

Proper citation: TIMER (RRID:SCR_018737) Copy   

•   Source: SciCrunch Registry

https://rvista.dcode.org/

Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites.

Proper citation: rVista (RRID:SCR_018707) Copy   

•   Source: SciCrunch Registry

https://hartleys.github.io/QoRTs/

Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R.

Proper citation: QoRTs (RRID:SCR_018665) 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

https://immunedb.readthedocs.io/en/latest/

Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features.

Proper citation: ImmuneDB (RRID:SCR_017125) Copy   

•   Source: SciCrunch Registry

https://github.com/Rinoahu/SwiftOrtho

Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.

Proper citation: SwiftOrtho (RRID:SCR_017122) Copy   

•   Source: SciCrunch Registry

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https://biit.cs.ut.ee/clustvis/

Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps.

Proper citation: ClustVis (RRID:SCR_017133) Copy   

•   Source: SciCrunch Registry

http://www.bio-rad.com/en-eh/product/cfx-manager-software

Software tool to analyze real-time PCR data and run PCR system in software controlled mode.

Proper citation: CFX Manager (RRID:SCR_017251) Copy   

•   Source: SciCrunch Registry

https://bioservices.uncc.edu

Core to assist with analyzing and interpreting data produced by genomic technologies.

Proper citation: University of North Carolina Charlotte Bioinformatics Services Division (RRID:SCR_017182) Copy   

•   Source: SciCrunch Registry

https://www.cityofhope.org/research/shared-resources/integrative-genomics-and-bioinformatics

Core provides genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators.

Proper citation: City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility (RRID:SCR_017188) Copy   

•   Source: SciCrunch Registry

https://www.hsph.harvard.edu/hmac/

Core assists with consultation for microbiome project development, provides validated meta omic analysis of microbial community data, and supports fully collaborative grant funded investigations.

Proper citation: Harvard School of Public Health Microbiome Analysis Core Facility (RRID:SCR_017187) Copy   

•   Source: SciCrunch Registry

https://github.com/ZSI-Bio/bdg-sequila

Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals.

Proper citation: SeQuiLa (RRID:SCR_017220) Copy   

•   Source: SciCrunch Registry

https://github.com/csbbcompbio/CSBB-v3.0

Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments.

Proper citation: Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) Copy   

•   Source: SciCrunch Registry