Tools   Select Another Resource Report Type

http://funcoup.sbc.su.se/search/

Database of genome wide functional coupling networks. Provides tools to explore predicted networks and to retrieve detailed information about data underlying each prediction. Web service for functional coupling search.

Proper citation: FunCoup (RRID:SCR_018711) Copy   

•   Source: SciCrunch Registry

https://github.com/GGFHF/NGScloud2

Software tool for RNA-seq analysis of non model species using cloud computing. Provides user friendly front end to operate Amazon hardware resources and to control workflows of bioinformatic analysis of de novo RNA-seq, reference-based RNA-seq and functional annotation specifically oriented to plant species.

Proper citation: NGScloud2 (RRID:SCR_018716) Copy   

•   Source: SciCrunch Registry

http://www.prisma-statement.org/

Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.

Proper citation: PRISMA (RRID:SCR_018721) Copy   

•   Source: SciCrunch Registry

http://www.consort-statement.org/

Standards for transparent trials reporting. Encompasses various initiatives developed by CONSORT Group to alleviate problems arising from inadequate reporting of randomized controlled trials. Main product of CONSORT is CONSORT Statement, which is evidence based, minimum set of recommendations for reporting randomized trials. CONSORT Statement is endorsed by medical journals and leading editorial organizations.

Proper citation: CONSORT (RRID:SCR_018720) Copy   

•   Source: SciCrunch Registry

http://nanotomy.org/

Large scale electron microscopy datasets. Large scale electron microscopy database for Human Type 1 Diabetes.

Proper citation: Nanotomy (RRID:SCR_018565) Copy   

•   Source: SciCrunch Registry

https://cole-trapnell-lab.github.io/monocle3/

Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points.

Proper citation: Monocle3 (RRID:SCR_018685) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/microfileplus

Software tool as microscopy image file format converter by MBF Bioscience. Converts common microscopy image files to JPEG2000 and OME-TIFF. Used to view, analyze, and share big image data from many sources.

Proper citation: MicroFilePlus (RRID:SCR_018724) Copy   

•   Source: SciCrunch Registry

http://doriclenses.com/life-sciences/software/955-doric-neuroscience-studio.html

Software tool which allows to control Doric hardware and acquire all required data simultaneously. Incorporates different modules for each devices connected.

Proper citation: Doric Neuroscience Studio (RRID:SCR_018569) Copy   

•   Source: SciCrunch Registry

http://www.softberry.com/berry.phtml?topic=fgenesh_plus_plus&group=help&subgroup=pipelines

Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software.

Proper citation: Fgenesh plus plus (RRID:SCR_018928) Copy   

•   Source: SciCrunch Registry

https://robetta.bakerlab.org/

Web tool as protein structure prediction service. Provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data. Produces model for entire protein sequence in presence or absence of sequence homology to protein of known structure.

Proper citation: Robetta (RRID:SCR_018805) Copy   

•   Source: SciCrunch Registry

http://protein.ict.ac.cn/FALCON/

Web tool as high throughput protein structure prediction service. High throughput server for protein structure prediction.

Proper citation: FALCON (RRID:SCR_018804) Copy   

•   Source: SciCrunch Registry

https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger

Software tool as set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants by 10x Genomics.

Proper citation: Long Ranger (RRID:SCR_018925) Copy   

•   Source: SciCrunch Registry

https://somapp.ucdmc.ucdavis.edu/pharmacology/bers/maxchelator/webmaxc/webmaxcE.htm

Web tool for computing metal ion concentrations in physiological solutions. Used for determining free metal concentration in presence of chelators or total metal given desired free concentration.

Proper citation: WEBMAXC EXTENDED (RRID:SCR_018807) Copy   

•   Source: SciCrunch Registry

https://inrae.github.io/ODAM/

Software experimental data table management system to make research data accessible and available for reuse with minimal effort on part of data provider. Allows any scientist or data researcher to be able to explore dataset and then extract some or all of data according to their needs. Designed to manage experimental data tables in quick and easy way for users.

Proper citation: ODAM (RRID:SCR_018774) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/software/elda/

Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly.

Proper citation: ELDA (RRID:SCR_018933) Copy   

•   Source: SciCrunch Registry

https://www.objtables.org

Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.

Proper citation: ObjTables (RRID:SCR_018652) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=trend

Software package includes tests for trends and change points detection. Used in analysis of environmental data.

Proper citation: trend (RRID:SCR_018658) Copy   

•   Source: SciCrunch Registry

https://github.com/aplbrain/saber

Library of containerized tools and workflow deployment system for enabling processing of large neuroimaging datasets. Provides canonical neuroimaging workflows specified in standard workflow language (CWL), integration with workflow execution engine (Airflow), imaging database (bossDB), and parameter database (Datajoint) to deploy workflows at scale, and tools to automate deployment and optimization of neuroimaging pipelines.

Proper citation: Scalable Analytics for Brain Exploration Research (RRID:SCR_018812) Copy   

•   Source: SciCrunch Registry

https://github.com/biocatiit/musclex

Software suite as collection of programs intended to assist with analyzing diffraction X-ray images. MuscleX diffraction X-ray image analyzing toolkit. Data reduction software for X-ray fiber diffraction data.

Proper citation: Muscle X (RRID:SCR_018811) Copy   

•   Source: SciCrunch Registry

https://github.com/Trinotate/Trinotate.github.io/wiki

Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

Proper citation: Trinotate (RRID:SCR_018930) Copy   

•   Source: SciCrunch Registry