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http://sourceforge.net/projects/bbmap

Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform.

Proper citation: BBmap (RRID:SCR_016965) Copy   

•   Source: SciCrunch Registry

http://zhoulab.usc.edu/TopDom/

Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TopDom (RRID:SCR_016964) Copy   

•   Source: SciCrunch Registry

http://www.lipidontology.com

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   

•   Source: SciCrunch Registry

https://anima.irisa.fr

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   

•   Source: SciCrunch Registry

https://plusconsortium.umn.edu

Research consortium from many different fields to plan, perform and analyze the studies that are needed to help researchers conduct future prevention and intervention for Lower Urinary Tract Symptoms (LUTS) in women.

Proper citation: Prevention of Lower Urinary Tract Symptoms (RRID:SCR_016923) Copy   

•   Source: SciCrunch Registry

https://commonfund.nih.gov/hubmap

Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows.

Proper citation: The Human BioMolecular Atlas Program (RRID:SCR_016922) Copy   

•   Source: SciCrunch Registry

http://dee2.io/

Software tool as a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive . DEE2 consists of three parts: Webserver where end-users can search for and obtain data-sets of interest, Pipeline that can download and process SRA data as well as users own fastq files, Back-end that collects, filters and organises data provided by contributing worker nodes.

Proper citation: Digital Expression Explorer 2 Project (RRID:SCR_016929) Copy   

•   Source: SciCrunch Registry

https://github.com/ToolsVanBox/smMIPfil

Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required.

Proper citation: smMIPfil (RRID:SCR_016892) Copy   

•   Source: SciCrunch Registry

https://github.com/zitmen/thunderstorm

Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging.

Proper citation: Thunder STORM (RRID:SCR_016897) Copy   

•   Source: SciCrunch Registry

https://crispr.cos.uni-heidelberg.de/

Web tool for CRISPR/Cas9 target prediction. Identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation.

Proper citation: CCTop (RRID:SCR_016890) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://kpmp.org

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www2.heatmapper.ca/

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   

•   Source: SciCrunch Registry

https://www.ccpn.ac.uk/

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   

•   Source: SciCrunch Registry

https://github.com/macmanes-lab/BinPacker/blob/master/README

Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.

Proper citation: BinPacker (RRID:SCR_017038) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry