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https://proteins.plus

Web portal for structure analysis of macromolecules.

Proper citation: ProteinPlus (RRID:SCR_022178) Copy   

•   Source: SciCrunch Registry

https://research.nhgri.nih.gov/hydractinia/

Portal provides genomic and transcriptomic data for researchers interested in Hydractinia genomics and molecular biology. Includes browsers for the H. symbiolongicarpus and H. echinata genome assemblies and interactive interface for interrogating H. symbiolongicarpus single cell gene expression atlas. Provides gene pages with functional annotation data for every gene model for both species, including protein domain composition and orthology predictions.

Proper citation: Hydractinia Genome Project Portal (RRID:SCR_022602) Copy   

•   Source: SciCrunch Registry

https://scorch.igs.umaryland.edu/

Data coordination, analysis, and scientific outreach center to standardize and share single cell molecular HIV/SUD data by ensuring that data is FAIR. Program with mission of generating resources that would enable comprehensive tissue characterization at single cell level. This includes generating single nucleus transcriptomic data for identification of novel rare cell types, and enrichment of key cellular populations to inform pathophysiological understanding of CNS effects of SUD and HIV. Interdisciplinary effort, involving teams of investigators at ten institutions including Yale, Boston University, Mount Sinai, University of Nebraska Medical Center, Broad Institute, University of California San Diego, Weill Cornell Medicine, Allen Institute, Scripps Research as well as a Data Coordination Center hosted at Institute for Genome Sciences, University of Maryland Baltimore School of Medicine.

Proper citation: SCORCH (RRID:SCR_022600) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/self-grooming-mice/

Portal provides protocol that implements JAABA, open source machine learning based behavior detection system; motr, open-source mouse trajectory tracking software; and bonsai, open source system capable of streaming and recording video. Together they use these tools to process videos of mice performing grooming behaviors in variety of behavioral setups.

Proper citation: Automated Classification of Self-grooming in Mice project (RRID:SCR_021597) Copy   

•   Source: SciCrunch Registry

https://lincsportal.ccs.miami.edu/signatures/home

Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures.

Proper citation: LINCS Data Portal 2.0 (RRID:SCR_022566) Copy   

•   Source: SciCrunch Registry

https://gitlab.orc.gmu.edu/kbijari/zebrafish-analysis-protocol

Project for quantitative neuronal morphometry by supervised and unsupervised learning. Includes protocol to quantify and interpret morphological properties of individual neurons reconstructed from microscopic imaging.Includes information about installation of analysis tools and downloading datasets and custom codes.

Proper citation: neuronal reconstruction analysis project (RRID:SCR_021638) Copy   

•   Source: SciCrunch Registry

https://www.fredhutch.org/en/research/shared-resources.html

Through Shared Resources, investigators in Fred Hutch/University of Washington Cancer Consortium and external academic and industry organizations can access services tailored to their specific research goals, including novel assay development or early access to new technologies.

Proper citation: Fred Hutchinson Cancer Center Shared Resources (RRID:SCR_022607) Copy   

•   Source: SciCrunch Registry

http://lipiddroplet.org/

Interactive portal provides datasets, across variety of cell types, for LD biology, including transcriptional profiles of induced lipid storage, organellar proteomics, genome-wide screen phenotypes, and ties to human genetics. Provides comprehensive picture of genes and pathways affecting lipid droplet biology, including gene expression, proteomics, and LD morphology phenotypes, by integrating multiple relevant data types.

Proper citation: Lipid Droplet Knowledge Portal (RRID:SCR_021650) Copy   

•   Source: SciCrunch Registry

https://www.utsouthwestern.edu/labs/danuser/software/

Software package as quantitative image analysis software for measurement of microtubule dynamics. MATLAB software for tracking full dynamics of microtubules based on plusTIP marker live cell image sequences.

Proper citation: plusTipTracker (RRID:SCR_021890) Copy   

•   Source: SciCrunch Registry

https://ror.org/

Community led project to develop open, sustainable, usable, and unique identifier for every research organization in the world. Implementation of ROR IDs in scholarly infrastructure and metadata will enable more efficient discovery and tracking of research outputs across institutions and funding bodies.

Proper citation: Research Organization Registry (RRID:SCR_021891) Copy   

•   Source: SciCrunch Registry

https://github.com/muriloHoracio/TERL

Software tool for classification of transposable elements by convolutional neural networks. Preprocesses and transforms one dimensional sequences into two dimensional space data, image like data of sequences, and apply it to deep convolutional neural networks.

Proper citation: TERL (RRID:SCR_022064) Copy   

•   Source: SciCrunch Registry

https://azphewas.com/

Repository of gene phenotype associations for phenotypes derived from electronic health records, questionnaire data, and continuous traits computed on exomes released by UK Biobank. Repository was made available by AstraZeneca for public research.

Proper citation: AstraZeneca PheWAS Portal (RRID:SCR_021643) Copy   

•   Source: SciCrunch Registry

https://www.cs.bham.ac.uk/~ibs/imzMLConverter/

Software tool for generating imzML. Allows conversion to imzML mass spectrometry imaging standard utilising mzML mass spectrometry standard as intermediary format.

Proper citation: imzMLConverter (RRID:SCR_021642) Copy   

•   Source: SciCrunch Registry

https://github.com/LaubachLab/MedParse

Software tool to read MedPC data into Python and Matlab. MedPC code for saving precise times of behavioral events and MatLab and Python functions to convert MedPC data into time event codes.

Proper citation: MedParse (RRID:SCR_021528) Copy   

•   Source: SciCrunch Registry

https://github.com/databricks/spark-xml

Software library for parsing and querying XML data with Apache Spark, for Spark SQL and DataFrames. XML data source for Spark SQL and DataFrames.

Proper citation: spark-xml (RRID:SCR_023636) Copy   

•   Source: SciCrunch Registry

https://github.com/elsevierlabs-os/spark-xml-utils

Software library to filter documents based on XPath expression, return specific nodes for XPath/XQuery expression, transform documents using XSLT stylesheet. By providing some basic wrappers to Saxon, spark-xml-utils library exposes some basic XPath, XQuery, and XSLT functionality that can readily be leveraged by any Spark application.

Proper citation: spark-xml-utils (RRID:SCR_023635) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-EUtilities

Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic.

Proper citation: Bio-EUtilities (RRID:SCR_024064) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Tools-Run-Alignment-Clustalw

Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.

Proper citation: Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/tab2mage/

Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.

Proper citation: Tab2MAGE (RRID:SCR_024101) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Tools-Phylo-PAML

Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.

Proper citation: Bio-Tools-Phylo-PAML (RRID:SCR_024069) Copy   

•   Source: SciCrunch Registry