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https://sedfitsedphat.nibib.nih.gov/software/default.aspx

Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.

Proper citation: SEDFIT (RRID:SCR_018365) Copy   

•   Source: SciCrunch Registry

http://pinet-server.org

Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.

Proper citation: piNET (RRID:SCR_018693) Copy   

•   Source: SciCrunch Registry

https://github.com/najasplus/hetindel_shinyapp

Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels.

Proper citation: Hetindel (RRID:SCR_018922) Copy   

•   Source: SciCrunch Registry

http://tools.dice-database.org/GOnet/)

Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.

Proper citation: GOnet (RRID:SCR_018977) Copy   

•   Source: SciCrunch Registry

http://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/license/

Software Matlab toolbox to perform representational similarity analysis for neural data.

Proper citation: Toolbox for Representational Similarity Analysis (RRID:SCR_019029) Copy   

•   Source: SciCrunch Registry

https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation

Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer.

Proper citation: CLIP Tool Kit (RRID:SCR_019034) Copy   

•   Source: SciCrunch Registry

https://www.openicpsr.org/openicpsr/covid19

Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings.

Proper citation: COVID-19 Data Repository (RRID:SCR_019105) Copy   

•   Source: SciCrunch Registry

https://usdrn.org/

Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies.

Proper citation: Urinary Stone Disease Research Network (RRID:SCR_019059) Copy   

•   Source: SciCrunch Registry

http://apid.dep.usal.es

APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.

Proper citation: Agile Protein Interactomes DataServer (RRID:SCR_008871) Copy   

•   Source: SciCrunch Registry

https://www.stat.auckland.ac.nz/~paul/plaudits/Iobion.htm

GeneTraffic is a web-based microarray data analysis and management software developed by Iobion Informatics that allows users to log onto a server, upload their microarray data and perform analysis and project management remotely. GeneTraffic was made by Iobion Informatics (now under Stratagene) and can be accessed thorough Internet Explorer 6.0 or greater on Windows XP.

Proper citation: GeneTraffic (RRID:SCR_008651) Copy   

•   Source: SciCrunch Registry

http://www.g-node.org/data

Platform for sharing data, with very large storage capability for electrophysiological data, EEG data is included. This service is provided for neuroscientists to facilitate data access, data storage, data analysis and data sharing. This service is developed and maintained by the German Node of the International Neuroinformatics Coordinating Facility. The global scale of neuroinformatics offers unprecedented opportunities for scientific collaborations between and among experimental and theoretical neuroscientists. To fully harvest these possibilities, coordinated activities are required to improve key ingredients of neuroscience: data access, data storage, and data analysis, together with supporting activities for teaching and training. Focusing on the development and free distribution of tools for handling and analyzing neurophysiological data, G-Node aims at addressing these aspects as part of the International Neuroinformatics Coordination Facility (INCF) and the German Bernstein Network for Computational Neuroscience (NNCN). G-Node also serves as an international forum for Computational Neuroscientists that are interested in sharing experimental data and tools for data analysis and modeling. G-Node is funded through the German Federal Ministry of Education and Research and hosted by Ludwig-Maximilians-Universit-Munchen.

Proper citation: G-node portal electrophysiology data sharing (RRID:SCR_008893) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/dbgapcleaner/

Tool to assist site staff with curation of data dictionary, data item, and subject item files for preparation to uploading and sharing data with DbGaP resource.

Proper citation: DbGaP Cleaner (RRID:SCR_009462) Copy   

•   Source: SciCrunch Registry

http://itools.loni.usc.edu/

An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).

Proper citation: iTools (RRID:SCR_009626) Copy   

•   Source: SciCrunch Registry

http://databrary.org/

Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data.

Proper citation: Databrary (RRID:SCR_010471) Copy   

•   Source: SciCrunch Registry

http://homer.ucsd.edu/

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

Proper citation: HOMER (RRID:SCR_010881) Copy   

•   Source: SciCrunch Registry

https://trials.bgcarlisle.com/

Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set.

Proper citation: Clinical Trials Viewer (RRID:SCR_019230) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/p/iris-scanning/calliope

Software package for image processing for MATLAB. Used for processing of calcium imaging data.

Proper citation: Calliope calcium imaging processing package (RRID:SCR_021213) Copy   

•   Source: SciCrunch Registry

https://cumulus.readthedocs.io/en/stable

Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.

Proper citation: Cumulus (RRID:SCR_021644) Copy   

•   Source: SciCrunch Registry

https://www.niaid.nih.gov/diseases-conditions/coronaviruses

Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses.

Proper citation: NIAID Overview of Coronaviruses (RRID:SCR_018290) Copy   

•   Source: SciCrunch Registry

https://github.com/davidaknowles/leafcutter/

Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs).

Proper citation: LeafCutter (RRID:SCR_017639) Copy   

•   Source: SciCrunch Registry