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http://www.illumina.com/

American company incorporated that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Provides a line of products and services that serve the sequencing, genotyping and gene expression and proteomics markets. Its headquarters are located in San Diego, California.

Proper citation: Illumina (RRID:SCR_010233) Copy   

•   Source: SciCrunch Registry

http://treestoolbox.org/

Software package, written in Matlab (Mathworks, Natick, MA), providing tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees. It provides the basic tools to edit, visualize and analyze dendritic and axonal trees, methods for quantitatively comparing branching structures between neurons, and tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance.

Proper citation: TREES toolbox (RRID:SCR_010457) Copy   

•   Source: SciCrunch Registry

https://www.bio-rad.com/en-us/product/bio-plex-200-systems?ID=715b85f1-6a4e-41b3-b5d9-80202d779e13

Suspension array system which offers protein and nucleic acid researchers multiplex assay solution permiting analysis of up to 100 biomolecules in single sample.

Proper citation: Bio-Rad: Bio-Plex 200 System (RRID:SCR_018026) Copy   

•   Source: SciCrunch Registry

https://pedsresearch.org/uploads/pages/img/LuminexManual_LX100.pdf

Flow cytometry analyzer system for individual labs that performs up to 100 different tests in single reaction volume and can use either magnetic beads or plain polystyrene beads.

Proper citation: Luminex: 100 Flow Cytometry Analyzer System (RRID:SCR_018025) Copy   

•   Source: SciCrunch Registry

http://www.eecs.qmul.ac.uk/mmv/datasets/deap/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 12,2025. Multimodal dataset for emotion analysis using EEG, Physiological and Video Signals of human affective states. The electroencephalogram (EEG) and peripheral physiological signals of 32 participants were recorded as each watched 40 one-minute long excerpts of music videos. Participants rated each video in terms of the levels of arousal, valence, like/dislike, dominance and familiarity. For 22 of the 32 participants, frontal face video was also recorded. A novel method for stimuli selection was used, utilizing retrieval by affective tags from the last.fm website, video highlight detection and an online assessment tool. The dataset is made publicly available and other researchers are encouraged to use it for testing their own affective state estimation methods.

Proper citation: DEAPdataset (RRID:SCR_001586) Copy   

•   Source: SciCrunch Registry

https://www.microscop.ru/uploads/Helios-NanoLab-600i-ds-web.pdf

Scanning Electron Microscope advanced DualBeam for ultra-high resolution imaging, analysis and fabrication at the nanoscale. Helios NanoLab 600i builds on the success of FEI’s winning DualBeam series offering advances in ion beam, electron beam, patterning and range of features to make milling, imaging, analysis and sample preparation down to nanoscale.

Proper citation: FEI: Helios Nanolab 600i DualBeam (RRID:SCR_027033) Copy   

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https://www.thermofisher.com/order/catalog/product/A45727

Ion Torrent Genexus Integrated Sequencer is part of the Ion Torrent Genexus System. Instrument that can automate library construction, templating, and sequencing in single-instrument run.

Proper citation: Thermo Fisher: Ion Torrent Genexus Integrated Sequencer (RRID:SCR_026449) Copy   

•   Source: SciCrunch Registry

http://www.broad.mit.edu/mpr/lung

Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.

Proper citation: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) Copy   

•   Source: SciCrunch Registry

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

Anatomical atlases constructed by Computational Anatomy of Johns Hopkins University for analysis of shape vectors. The atlases were generated from segmented hippocampal and amygdala structures in acquired populations of children, adolescents and young adults in neuroimaging studies of major depression disorder (MDD) at Washington University at St Louis.

Proper citation: Atlases of amygdala and hippocampus for pediatric populations (RRID:SCR_014085) Copy   

•   Source: SciCrunch Registry

http://mzmatch.sourceforge.net/

A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java.

Proper citation: mzMatch (RRID:SCR_000543) Copy   

•   Source: SciCrunch Registry

http://www.rstudio.com/shiny/

Open source R package that provides web framework for building web applications using R. Used to create interactive web apps in native R, without needing to use HTML, CSS, or JavaScript.

Proper citation: Shiny (RRID:SCR_001626) Copy   

•   Source: SciCrunch Registry

https://pepatac.databio.org/en/latest/

Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats.

Proper citation: PEPATAC (RRID:SCR_024758) Copy   

•   Source: SciCrunch Registry

https://github.com/DiogoVeiga/maser

Software package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events. Mapping alternative splicing events to proteins.

Proper citation: maser (RRID:SCR_023484) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/metagear/index.html

Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis.

Proper citation: metagear (RRID:SCR_017085) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry

https://github.com/theislab/scvelo

Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling.

Proper citation: scVelo (RRID:SCR_018168) Copy   

•   Source: SciCrunch Registry

https://covic.lji.org/databases/

Serves as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. Most potent antibodies will guide development of vaccines to stop current outbreak and protect against future pandemics.

Proper citation: CoVIC-DB Database (RRID:SCR_018339) Copy   

•   Source: SciCrunch Registry

http://www.icpsr.umich.edu/SAMHDA/

Database of the nation''s substance abuse and mental health research data providing public use data files, file documentation, and access to restricted-use data files to support a better understanding of this critical area of public health. The goal is to increase the use of the data to most accurately understand and assess substance abuse and mental health problems and the impact of related treatment systems. The data include the U.S. general and special populations, annual series, and designs that produce nationally representative estimates. Some of the data acquired and archived have never before been publicly distributed. Each collection includes survey instruments (when provided), a bibliography of related literature, and related Web site links. All data may be downloaded free of charge in SPSS, SAS, STATA, and ASCII formats and most studies are available for use with the online data analysis system. This system allows users to conduct analyses ranging from cross-tabulation to regression without downloading data or relying on other software. Another feature, Quick Tables, provides the ability to select variables from drop down menus to produce cross-tabulations and graphs that may be customized and cut and pasted into documents. Documentation files, such as codebooks and questionnaires, can be downloaded and viewed online.

Proper citation: Substance Abuse and Mental Health Data Archive (RRID:SCR_007002) Copy   

•   Source: SciCrunch Registry

http://pepr.cnmcresearch.org/

An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ).

Proper citation: Public Expression Profiling Resource (RRID:SCR_007274) Copy   

•   Source: SciCrunch Registry

http://pbil.univ-lyon1.fr/acuts/ACUTS.html

THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Database that identifies new regulatory elements in untranslated regions of protein-coding genes (5 prime flanks, 5 prime UTRs, introns, 3 prime UTRs and 3 prime flanks). The analyses is focused on genes from metazoan species (essentially vertebrates, insects and nematodes). Information on highly conserved regions (sequences, alignments, annotations, bibliographic references) are compiled. Currently 176 out of 326 detected highly conserved regions (HCRs) have been analyzed and incorporated in the database. You can also access the list of annotated conserved elements and the list of conserved elements that remain to be processed. Their approach is based on comparative sequence analysis, for the identification of phylogenetic footprints.

Proper citation: Ancient conserved untranslated sequences (RRID:SCR_008130) Copy   

•   Source: SciCrunch Registry