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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/sanket-desai/InfectiousPathogenDetector2
IPD2 is updated version of InfectiousPathogenDetector, in-silico GUI-based automated pathogen analysis pipeline for seamless analysis of data from heterogenous NGS platforms. IPD performs integrated variants analysis, along with systematic quantification of pathogen genomes. IPD additionally has an in-built SARS-CoV-2 analysis module, for assignment of viral clades of the samples analyzed and an automated report generation.
Proper citation: InfectiousPathogenDetector2 (RRID:SCR_026220) Copy
https://github.com/Lin-Xu-lab/SpaSNE.git
Software extension of t-distributed stochastic neighbor embedding, the spatially resolved t-SNE (SpaSNE) designed to preserve both global gene expression and spatial structure for spatially resolved profiling data. Gives comprehensive low-dimensional visualization that could best reflect the molecular similarities of cells and the spatial interactions between cells.
Proper citation: SpaSNE (RRID:SCR_026223) Copy
https://webbook.nist.gov/chemistry/
Database that provides access to organic compounds data compiled and distributed by NIST under the Standard Reference Data Program.
Proper citation: NIST Chemistry WebBook (RRID:SCR_026225) Copy
https://winscp.net/eng/download.php
Free file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, and secure copy protocol client for Microsoft Windows.
Proper citation: WinSCP (RRID:SCR_026226) Copy
https://centers.louisville.edu/brown-cancer-center/core-facilities/molecular-modeling
Core offers services including molecular modeling of proteins and nucleic acids, virtual drug screening, computational biophysics.
Proper citation: University of Louisville School of Medicine Molecular Modeling Core Facility (RRID:SCR_026183) Copy
Software application for statistical calculation.
Proper citation: 2015 PQStat Statistical Calculation Software (RRID:SCR_026338) Copy
https://genomics.ucsf.edu/ucsf-clinical-cancer-genomic-laboratory
Core performs standard-of-care and advanced molecular testing for patients with cancer, and to provides special expertise in solid tumors. Services include targeted gene sequencing, microsatellite instability testing, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS). CCGL is staffed with board-certified surgical pathologists and board-certified molecular pathologists who can properly evaluate the quality of samples submitted for testing as well as make correlations between the pathologic diagnosis of a tumor and the molecular findings in the tumor.
Proper citation: University of California San Francisco Clinical Cancer Genomics Laboratory Core Facility (RRID:SCR_026219) Copy
https://github.com/YingMa0107/CARD/
Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations.
Proper citation: Conditional AutoRegressive Deconvolution (RRID:SCR_026310) Copy
https://mcw.ilab.agilent.com/service_center/5443/?tab=about
Institutionally available research service unit managed on behalf of the Medical College by the Department of Cell Biology, Neurobiology and Anatomy. OCAM-EM encompasses both Light and Electron Microscopy services.
Proper citation: Medical College of Wisconsin Oxford Instruments Center for Advanced Microscopy Electron Microscopy Core Facility (RRID:SCR_026315) Copy
https://sites.google.com/ualberta.ca/phhl/home
Core to advance understanding of mechanism of vascular dysfunction in chronic disease, identify how vascular dysfunction contributes to exercise intolerance, evaluate how exercise training improves vascular dysfunction and exercise intolerance using innovative clinical trial designs.
Proper citation: University of Alberta Precision Human Health Laboratory Core Facility (RRID:SCR_026314) Copy
Portal provides access to cancer genomic data from variety of analyses: clinical, copy number, miR, miRseq, mRNA, mRNAseq, mutation and pathway analyses. Provides comprehensive suite of interdependent analyses of those data, including: correlations, clustering, and GISTIC and MutSigCV. Companion portal to the Broad Institute GDAC Firehose analysis pipeline, and was developed to cull and analyze data generated by The Cancer Genome Atlas (TCGA), which characterizes and identifies genomic patterns in human cancer models.
Proper citation: FireBrowse (RRID:SCR_026320) Copy
Portal provides information about nationwide study of more than 50,000 individuals to determine factors that predict disease severity and long-term health impacts of COVID-19.
Proper citation: Collaborative Cohort of Cohorts for COVID-19 Research (RRID:SCR_026322) Copy
https://github.com/labcbb/SqueezeCall
Software tool as Nanopore basecalling using Squeezeformer network to improve basecalling accuracy over recurrent neural network (RNN)-based model and Transformer-based models.
Proper citation: SqueezeCall (RRID:SCR_026321) Copy
https://dsigdb.tanlab.org/DSigDBv1.0/
Online database provides collection of gene sets based on quantitative inhibition and/or drug-induced gene expression changes data of drugs and compounds. Allows users to search, view and download drugs/compounds and gene sets.
Proper citation: DSigDB (RRID:SCR_026202) Copy
https://github.com/biocheming/watvina
Software tool as implicit or explicit water model based docking with Autodock vina engine, supporting pharmacophore /position constrained docking.Facilitates drug design with support for explicit or implicit waters, pharmacophore or position-constrained docking, and external torsion parameters (akin to amber/gaff/charmm force fields). Water Model supported protein-ligand docking with Autodock Vina engine.
Proper citation: watvina (RRID:SCR_026282) Copy
https://github.com/zengxiaofei/HapHiC
Software fast, reference-independent, allele-aware scaffolding tool based on Hi-C data. Allele-aware scaffolding tool that uses Hi-C data to scaffold haplotype-phased genome assemblies into chromosome-scale pseudomolecules.
Proper citation: HapHiC (RRID:SCR_026284) Copy
http://qualimap.conesalab.org/
Software platform-independent application written in Java and R that provides both Graphical User Inteface and command-line interface to facilitate quality control of alignment sequencing data and its derivatives like feature counts. Used for advanced multi-sample quality control for high-throughput sequencing data.
Proper citation: Qualimap 2 (RRID:SCR_026258) Copy
Web isotopologue analysis tool for metabolomics experiment. Used to compute tracer analysis. Transforms raw mass spec AUC values into the percent representation of each isotopologue measured.
Proper citation: Fluxfix (RRID:SCR_026259) Copy
https://github.com/parklab/MuSiCal
Software Python toolkit for mutational signature analysis. Used to estimate mutational signatures from somatic mutations in genome.
Proper citation: MuSiCal (RRID:SCR_026265) Copy
https://github.com/mskcc/facets
Software tool for estimating genome copy numbers from high throughput DNA sequencing data. Allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Used to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
Proper citation: FACETS (RRID:SCR_026264) Copy
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