Curator Dashboard

NITRC-IR Test is for invited individuals to test the NITRC-Image Repository Beta functionality and provide the NITRC team feedback feed before making this functionality fully public.

• Resource
• NIF
• 7 months ago - by Anonymous

Software accurate read-based phasing tool that integrates multiple methodologies to enhance phasing accuracy. Used to efficiently phase genomic data by linking sequencing reads across heterozygous sites, extending haplotype blocks, and incorporating pre-phased data when available. Read-based phasing algorithm with integrated multi-method support for enhanced accuracy.

• Resource
• RRID
• 7 months ago - submitted by Uri Hartmann

Multiphoton imaging system for deep imaging in biological tissue. For advanced applications,dual-wavelength excitation extending to 1300 nm is available. Independent control of visible or multiphoton laser light stimulation and ability to synchronize with patch clamp data are also possible. Multiple configurations are available.

• Resource
• RRID
• 7 months ago - submitted by Edyta Vieth

Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Facility imaging system offers stable imaging conditions, especially crucial for high magnification and time-dependent studies. Z2m model is optimized for materials science applications. It is often used for tasks like 3D subsurface studies of transparent ceramics, metallography, corrosion studies, analysis of thin film uniformity, and inclusion analysis in metals. It is particularly well-suited for situations that require motorized stage to handle large samples.

• Resource
• RRID
• 7 months ago - submitted by Edyta Vieth

Software pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT. Used to quickly screen for transferred genes.

• Resource
• RRID
• 7 months ago - by Anonymous

Software phylogenomic pipeline designed to analyze proteomes from diverse organisms and inferring orthology, gene-family trees, and species tree. Highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionar history. Efficiently performs phylogenetic comparisons at any evolutionary scale.

• Resource
• RRID
• 7 months ago - by Anonymous

Software pipeline to build similarity maps of protein space. Identifies proteins related to query protein using sequence- and structure-based searches, compares all protein structures, and creates navigable map that can be used to look at protein relationships and make hypotheses about function.

• Resource
• RRID
• 7 months ago - by Anonymous

Software R package that supports different types of gene set enrichment workflows. Offers multiple enrichment, visualization, and sharing methods in addition to novel features such as hierarchical geneset analysis and built-in markdown reporting.

• Resource
• RRID
• 7 months ago - by Anonymous

Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Leica confocal imaging system designed to maximize number of probes and photon collection sensitivity for wide range of applications, including fixed and live samples

• Resource
• RRID
• 7 months ago - submitted by Edyta Vieth

Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Leica TCS SP8 system located in Icahn Building is high precision confocal microscope for live cell imaging in multicolor. Advanced confocal inverted imaging platform for fixed- and live-cell studies. This system features seven laser excitation lines; motorized stage for multi-position imaging; advanced detection system for spectral unmixing; and full incubation setup for long-term research.

• Resource
• RRID
• 7 months ago - submitted by Edyta Vieth

Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Leica TCS SP8 system is high precision confocal microscope with Acousto-Optical Beam Splitter that allows for flexible control of the excitation and emission light paths.

• Resource
• RRID
• 7 months ago - submitted by Edyta Vieth

Dragonfly spinning disk confocal microscopy system. Andor Dragonfly 600 series high-contrast multi-dimensional imaging platform for live cell imaging. Andor Dragonfly 620 is spinning disk confocal with many advanced modalities capable of widefield imaging, high-sensitivity or high-contrast spinning disk imaging, TIRF (critical angle, Hi-Lo), STORM (single molecule imaging), photostimulation of specific cellular regions and dual-camera recording.

• Resource
• RRID
• 7 months ago - submitted by Edyta Vieth

Software repository provides the code for generalizable machine learning models for rapid antimicrobial resistance prediction in unseen healthcare settings.

• Resource
• RRID
• 7 months ago - by Anonymous

Software toolkit containing lots of useful tools for genomics analyses. Used to check, fix, pad missing information (features/attributes) of any kind of GTF and GFF to create complete, sorted and standardised gff3 format.

• Resource
• RRID
• 7 months ago - by Anonymous

Core to procure and coordinate distribution of fresh frozen human tissue in optimal state of preservation for requesting investigators without impacting diagnostic quality, accuracy and safety in anatomic pathology. Additional services offered include biospecimen DNA or RNA extraction, sectioning of frozen tissues, short-term tissue culture, cytogenetic/molecular cytogenetic analysis, and tissue preparation via investigator-driven protocols.

• Resource
• RRID
• 7 months ago - by Anonymous

Software R package defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users.

• Resource
• RRID
• 7 months ago - by Anonymous

Software R package to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers. Can also be used to read data from .loom files.

• Resource
• RRID
• 7 months ago - by Anonymous

Software package for computing collection of clustering validation or quality criteria and partition comparison indices.

• Resource
• RRID
• 7 months ago - by Anonymous

Software Python package for handling mmCIF and BinaryCIF files compliant with the ModelCIF extension.

• Resource
• RRID
• 7 months ago - by Anonymous

Software pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. FIJI macro for quantifying pattern in extracellular matrix.

• Resource
• RRID
• 7 months ago - by Anonymous