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http://crispr.hzau.edu.cn/CRISPR/

Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment.

Proper citation: CRISPR-P (RRID:SCR_016941) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/macromodel

Software package for molecular modeling. Computes free energy changes using free energy perturbation method. Used to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex.

Proper citation: MacroModel (RRID:SCR_016747) Copy   

•   Source: SciCrunch Registry

https://github.com/Crick-CancerGenomics/ascat

Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data.

Proper citation: ascat (RRID:SCR_016868) Copy   

•   Source: SciCrunch Registry

https://blake.bcm.edu/emanwiki/EMAN2

Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography.

Proper citation: EMAN (RRID:SCR_016867) Copy   

•   Source: SciCrunch Registry

https://github.com/aroth85/pyclone

Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing.

Proper citation: Pyclone (RRID:SCR_016873) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/shape-screening

Software tool for shape-based superposition and similarity searching. Identifies new compounds with shapes (and, if desired, other properties) that are similar to the known binder.

Proper citation: Shape screening (RRID:SCR_016750) Copy   

•   Source: SciCrunch Registry

https://github.com/reinkk/Metab

Software package as a metabolomic data processing pipeline in R codes.

Proper citation: Metab (RRID:SCR_016877) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://bionanogenomics.com/wp-content/uploads/2017/01/30047-Irys-User-Guide.pdf

System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies.

Proper citation: BioNano: Irys system (RRID:SCR_016754) Copy   

•   Source: SciCrunch Registry

https://knoweng.org

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   

•   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

https://github.com/NIMML/ENISI-MSM

Software tool for simulating the mucosal immune responses to Helicobacter pylori infection in stomach.

Proper citation: ENteric Immunity SImulator (ENISI) Multi scale model (RRID:SCR_016918) 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://csgid.org/csgid/metal_sites

Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal.

Proper citation: CheckMyMetal (RRID:SCR_016887) 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

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.uni-muenster.de/de/

The University of Münster is a public university located in the city of Münster, North Rhine-Westphalia in Germany. It is Germany fifth largest university.

Proper citation: University of Muenster; Muenster; Germany (RRID:SCR_016853) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry