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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://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

https://github.com/TGAC/KAT

Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies.

Proper citation: KAT (RRID:SCR_016741) Copy   

•   Source: SciCrunch Registry

https://micro-manager.org/

Software package for control of automated microscopes. Cross-platform desktop application, to control a motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories.

Proper citation: μManager (RRID:SCR_016865) 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

http://southgreen.fr/content/gigwa

Web tool to explore genotyping metdata by filtering it on basis of variant features, including functional annotations and matching genotype patterns. May be deployed on workstation or as data portal. Allows to feed MongoDB database with VCF, PLINK or HapMap files and provides interface to filter data in real time. Used to export filtered data into formats and features connectivity with online genomic tools and with standalone software such as FlapJack or IGV. Gigwa hosted datasets are interoperable via two standard REST APIs such GA4GH and BrAPI.

Proper citation: Gigwa (RRID:SCR_017080) Copy   

•   Source: SciCrunch Registry

https://github.com/kendomaniac/rCASC

Software package for reproducible classification analysis of single cell sequencing data.

Proper citation: rCASC (RRID:SCR_017005) Copy   

•   Source: SciCrunch Registry

https://neurobot.incf.org

Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis.

Proper citation: INCF-Neurobot (RRID:SCR_017004) Copy   

•   Source: SciCrunch Registry

https://www.stemformatics.org/#

Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data. Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others.

Proper citation: Stemformatics (RRID:SCR_017002) Copy   

•   Source: SciCrunch Registry

http://scikit-criteria.org/en/latest/

Software tool as collection of Multiple Criteria Decision Analysis methods integrated into scientific Python stack.

Proper citation: Scikit-Criteria (RRID:SCR_017084) Copy   

•   Source: SciCrunch Registry

https://link.springer.com/article/10.1007%2Fs00424-017-2067-y

Integrated circuit device used as tool for amperometry measurement as replacement of conventional carbon fiber microelectrode. Surface modified structures with SU 8 microwells increases life span of each individual device and achieves single cell measurement efficiency by trapping cells inside microwells.

Proper citation: Surface Modified Amperometry CMOS IC (RRID:SCR_017082) Copy   

•   Source: SciCrunch Registry

https://github.com/lucapinello/Haystack

Software suite of computational tools implemented in Python to study epigenetic variability, cross cell type plasticity of chromatin states and transcription factors motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation. Epigenetic variability and transcription factor motifs analysis pipeline.

Proper citation: Haystack (RRID:SCR_017087) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/fenderglass/Flye

Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms.

Proper citation: Flye (RRID:SCR_017016) Copy   

•   Source: SciCrunch Registry

https://www.olympus-global.com/news/2016/nr160405fv3000e.html

FV3000 is a laser scanning confocal microscope system that captures high-resolution, high-contrast images by scanning samples point by point, enabling precise 3D fluorescence imaging. The system supports inverted and upright configurations and accommodates various objectives with magnifications ranging from 1.25× to 100×, including oil, silicone, and dry lenses, which allows imaging of both macro and micro-scale samples. It is equipped with multiple laser lines for excitation, including 405 nm, 488 nm, 561 nm, and 640 nm, as well as additional lines in some configurations (445 nm, 514 nm, 594 nm, 630 nm), enabling the use of several fluorophores simultaneously. On the detection side, the microscope uses high-sensitivity photomultiplier tube detectors, including GaAsP PMTs and multi-alkali PMTs.

Proper citation: Olympus: FluoView FV3000 Confocal Laser Scanning Microscope (RRID:SCR_017015) Copy   

•   Source: SciCrunch Registry