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http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Data analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast.

Proper citation: BLASTP (RRID:SCR_001010) Copy   

•   Source: SciCrunch Registry

http://blogs.plos.org/

PLoS Blogs has been set up to bring a select group of independent science and medicine bloggers together with the editors and staff who run our blogs. Our independent network is made up of writers who love science and medicine, and scientists and physicians that love to write. Here, you'll find an equal mix of blogs from journalists and researchers tackling diverse issues in science and medicine. There are three very distinct types of blogs on the PLoS Blogs network: the official PLoS blog, the PLoS journal blogs (collectively known as The PLoS Blogs), and blogs from the independent network (a.k.a. The PLoS Blogosphere) # The official PLoS blog: This content is produced, edited, and/or maintained by PLoS staff. # The journal blogs: This content is produced, edited, and/or maintained by PLoS journal staff: The current journal blogs are Speaking of Medicine (PLoS Medicine's blog) and everyONE (PLoS ONE's blog). # Our independent network of bloggers (The PLoS Blogosphere): This content is produced, edited, and/or maintained by the authors. * All of the content in The PLoS Blogosphere came from the minds of the authors. PLoS does not screen, edit, or otherwise meddle with content on the these blogs in any way. Our bloggers and our users are held to exactly the same standards, and the community guidelines apply to everyone that uses our site. If a blogger has posted content that you believe violates our site abuse policy, please contact PLoS. * Bloggers monitor their own comment threads: All comments will be reviewed by the author of the blog where you leave your thoughts. Just follow our simple community guidelines and we'll all get along just fine.

Proper citation: PLoS Blogs (RRID:SCR_001371) Copy   

•   Source: SciCrunch Registry

http://www.btool.org/WegoLoc

Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information.

Proper citation: WegoLoc (RRID:SCR_001402) Copy   

•   Source: SciCrunch Registry

http://igenbio.com/

A web-based genome analysis platform that integrates proprietary functional genomic data, metabolic reconstructions, expression profiling, and biochemical and microbiological data with publicly available information. Focused on microbial genomics, it provides better and faster identification of gene function across all organisms. Building upon a comprehensive genomic database integrated with a collection of microbial metabolic and non-metabolic pathways and using proprietary algorithms, it assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways and gene products. . * Automated and manual annotation of genes and genomes * Analysis of metabolic and non-metabolic pathways to understand organism physiology * Comparison of multiple genomes to identify shared and unique features and SNPs * Functional analysis of gene expression microarray data * Data-mining for target gene discovery * In silico metabolic engineering and strain improvement

Proper citation: ERGO (RRID:SCR_001243) Copy   

•   Source: SciCrunch Registry

http://www.itmat.upenn.edu/cohsi.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Informatics core for the purpose of promoting clinical research by collecting data from the Penn Health System.

Proper citation: Penn Community Outreach Using Health System Informatics Core (RRID:SCR_000304) Copy   

•   Source: SciCrunch Registry

https://psignifit.sourceforge.net/

Software toolbox to fit psychometric functions and to test hypotheses about psychometric data.

Proper citation: psignifit (RRID:SCR_024196) Copy   

•   Source: SciCrunch Registry

http://metabarcoding.org/sumaclust

Software tool aims to cluster sequences in a way that is fast and exact at the same time.

Proper citation: sumaclust (RRID:SCR_024352) Copy   

•   Source: SciCrunch Registry

https://ice.synthego.com/#/

Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data.

Proper citation: Inference of CRISPR Edits (RRID:SCR_024508) Copy   

•   Source: SciCrunch Registry

http://datacite.labs.orcid-eu.org

Service (Beta) that allows users to search the DataCite Metadata Store, and add their research outputs including datasets, software, and others to their ORCID profile. This should increase the visibility of these research data, and will make it easier to use these data citations in applications that connect to the ORCID Registry. In addition, the service is also providing formatted citations in several popular citation styles, supports COinS, links to related resources, and displays the attached Creative Commons license where this information is available. The DataCite Metadata Store of course also contains many text documents from academic publishers and services such as figshare or PeerJ Preprints, and these works can also be claimed. This tool is a collaborative effort by ORCID, CrossRef and DataCite.

Proper citation: ODIN (RRID:SCR_001386) Copy   

•   Source: SciCrunch Registry

http://www.genetics.med.ed.ac.uk/blog/

This resource aims to provide information for the general public on the background and current progress of scientific research into the role of genetics in these disorders. Additionally, it also aims to provide a forum for the discussion of aspects of psychiatric genetics open to members of the research community.

Proper citation: Schizophrenia and Bipolar Disorder Genetics Blog (RRID:SCR_001541) Copy   

•   Source: SciCrunch Registry

http://neuralensemble.org/sumatra/

A software tool for managing and tracking projects based on numerical simulation or analysis to support reproducible research. It can be thought of as an automated electronic lab notebook for simulation/analysis projects. Sumatra consists of: a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the context, annotating these records, linking to data files, etc.; a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results; a LaTeX package and Sphinx extension for including Sumatra-tracked figures and links to provenance information in papers and other documents; and a Python API, on which smt and smtweb are based, that can be used in personalized scripts in place of using smt.

Proper citation: Sumatra (RRID:SCR_001381) Copy   

•   Source: SciCrunch Registry

https://www.bioinformatics.nl/cgi-bin/emboss/getorf

Web application to find and extract open reading frames (ORFs). Used to find and output sequences of open reading frames in one or more nucleotide sequences.

Proper citation: getorf (RRID:SCR_024691) Copy   

•   Source: SciCrunch Registry

https://www.photometrics.com/products/ocular

Photometrics acquisition software to capture, save and publish images and movies. Allows users of color and monochrome cameras to capture high quality images and videos from their microscope or lens system.

Proper citation: Ocular (RRID:SCR_024467) Copy   

•   Source: SciCrunch Registry

https://github.com/qiyueyang-7/scNTImpute.git

Software imputation model for scRNA-seq data. Used to accurately and efficiently identify dropout values and impute them precisely, which helps to improve downstream analyses of single-cell RNA sequencing data.

Proper citation: scNTImpute (RRID:SCR_024395) Copy   

•   Source: SciCrunch Registry

https://github.com/GreenleafLab/ChrAccR

Software R package for comprehensive analysis chromatin accessibility data. Analyzing chromatin accessibility data in R. Used for data quality control, exploratory analyses including unsupervised methods for dimension reduction, clustering and quantifying transcription factor activities, and identification and characterization of differentially accessible regions. Used for analysis of large bulk datasets comprising hundreds of samples as well as for single cell datasets.

Proper citation: ChrAccR (RRID:SCR_024397) Copy   

•   Source: SciCrunch Registry

https://portal.brain-map.org/atlases-and-data/bkp/mapmycells

MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells.

Proper citation: MapMyCells (RRID:SCR_024672) Copy   

•   Source: SciCrunch Registry

https://github.com/STOmics/EAGS

Software tool for high resolved spatial transcriptomics. Smoothing approach for spatial transcriptome data with ultrahigh resolution. Used to determine neighborhood relationship of cells, to calculate smoothing contribution to recalculate the gene expression of each cell.

Proper citation: Efficient and Adaptive Gaussian Smoothing (RRID:SCR_024399) Copy   

•   Source: SciCrunch Registry

https://www.olympus-lifescience.com/en/downloads/detail-iframe/?0[downloads][id]=847249651

Software for image processing. Reads data captured by FV1200/FV1000/FV500/FV300 microscopes. Images saved with FV file format (OIF, OIB, FV Multi-Tiff) can be read.

Proper citation: Olympus FV10-ASW Viewer (RRID:SCR_024433) Copy   

•   Source: SciCrunch Registry

http://mpds.neist.res.in:8085/

Galaxy based disease specific web portal for drug discovery research of COVID-19. Open access disease specific drug discovery portal.

Proper citation: Molecular Property Diagnostic Suite Covid-19 (RRID:SCR_024545) Copy   

•   Source: SciCrunch Registry

https://prosite.expasy.org/scanprosite/

Web tool for detecting PROSITE signature matches in protein sequences.

Proper citation: ScanProsite (RRID:SCR_024425) Copy   

•   Source: SciCrunch Registry