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https://github.com/reinkk/Metab
Software package as a metabolomic data processing pipeline in R codes.
Proper citation: Metab (RRID:SCR_016877) Copy
https://github.com/PatternRecognition/OpenBMI
Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time.
Proper citation: OpenBMI (RRID:SCR_016876) Copy
Part of the NIH Big Data to Knowledge (BD2K) Initiative. One of 11 Centers of Excellence in Big Data Computing. Platform for genomics data analysis where user-supplied data sets will be analyzed in the context of existing knowledge. E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data.
Proper citation: KnowEnG (RRID:SCR_016875) Copy
https://github.com/dpeerlab/phenograph
Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.
Proper citation: Phenograph (RRID:SCR_016919) Copy
http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.
Proper citation: clusterProfiler (RRID:SCR_016884) Copy
Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States.
Proper citation: Kidney Precision Medicine Project (RRID:SCR_016920) Copy
https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/
Software tool for trimming and filtering sequencing data. Used to combine data quality related trimming, filtering, and masking operations into a single tool adapter. BBDuk2 allows multiple kmer based operations in a single pass.
Proper citation: Bestus Bioinformaticus Duk (RRID:SCR_016969) Copy
https://picrust.github.io/picrust/
Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome.
Proper citation: PICRUSt (RRID:SCR_016855) Copy
http://bioconductor.org/packages/release/data/experiment/html/affydata.html
Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.
Proper citation: affydata (RRID:SCR_016976) Copy
http://www.nitrc.org/projects/quicknii/
Histological brain section series aligner to volumetric atlases. Software tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems. Part of the QUINT workflow.
Proper citation: QuickNII (RRID:SCR_016854) Copy
Software tool to create and provide heat maps through a graphical interface. Allows to create an expression, pairwise comparison, image overlay, geomap, and geocoordinate heat maps for different data types and applications. Used to interactively visualize data.
Proper citation: Heatmapper (RRID:SCR_016974) Copy
Project provides tools and knowledge to maximize the impact of the biological NMR studies. CCPN software facilitates data analysis and software integration. Project promotes the exchange of knowledge and provides training and best practices for the NMR community and has leading role in the development of NMR data sharing standard and coordination of NMR instrumentation proposals. Includes CCPN Data Model for macromolecular NMR and related areas, CcpNmr suite of programs like Analysis for spectrum visualization, resonance assignment and analysis, ChemBuild to create chemical structure templates in an NMR aware manner, FormatConverter for data exchange with common textual NMR formats and SpecView for swift, format independent peak and spectrum visualization.
Proper citation: Collaborative Computing Project for NMR (RRID:SCR_016983) Copy
https://www.ccpn.ac.uk/v2-software/software/extras/datamodelfolder
Model to cover data for macromolecular NMR spectroscopy from the initial experimental data to the final validation. Used for the large scale data deposition, data mining and program interoperability. Enables movement from one software package to another without difficulties with data conversion or loss of information. Works with CcpNmr Analysis software for analysis and interactive display, CcpNmr FormatConverter for allowing transfer of data from programs used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment. Used within the CCPN software suite for NMR spectroscopy and at the BioMagResBank for converting existing deposited restraint lists to a standard IUPAC nomenclature.
Proper citation: CCPN Data Model (RRID:SCR_016982) Copy
https://www.ccpn.ac.uk/v2-software/software/analysis
Software package for interactive NMR spectrum visualization, resonance assignment and data analysis. Graphical elements allow to enter information and to view status of data and library functions manipulate the CCPN data model objects to record the scientific information. Software is cross platform and works on Linux, Mac OSX, Windows and Unix.
Proper citation: CCPN Analysis (RRID:SCR_016984) Copy
http://ced.co.uk/products/sigovin
Software package for sweep based data acquisition and analysis of time based waveform data obtained through CED digital analogue converter by Cambridge Electronic Design System Limited. Used for transient capture, patch and voltage clamp, LTP studies, evoked response and TMS.
Proper citation: Signal (RRID:SCR_017081) Copy
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
http://bioconductor.org/packages/CATALYST/
Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation.
Proper citation: CATALYST (RRID:SCR_017127) Copy
https://github.com/cancerit/cgpBattenberg
Software tool as installation helper, perl wrapper and R program Battenberg which detects subclonality and copy number in matched NGS data.
Proper citation: cgpBattenberg (RRID:SCR_017092) Copy
Web based ontology enrichment tool for lipidomic data analysis. Used for lipidomics to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and organelle associations. Freely accessible in a platform independent way.
Proper citation: LION/web (RRID:SCR_017018) Copy
Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows.
Proper citation: Anima (RRID:SCR_017017) Copy
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