Tools   Select Another Resource Report Type

https://huygens.science.uva.nl/PlotTwist/

Web application for plotting and annotating continuous data. Open source web app for plotting and annotating time series data. Used to inspect data and generate publication quality visualizations. Available options for plotting include lineplot, small multiples and heatmap, summary statistics and inferential statistics.

Proper citation: PlotTwist (RRID:SCR_018331) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SpydrPick

Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree.

Proper citation: SpydrPick (RRID:SCR_018176) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SuperDCA

Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis.

Proper citation: SuperDCA (RRID:SCR_018175) Copy   

•   Source: SciCrunch Registry

https://github.com/BackofenLab/CRISPRcasIdentifier

Software tool providing machine learning approach for identification and classification of CRISPR-Cas systems. Combines regression and classification approaches for improving quality of input protein cassettes and predicting their subtypes.

Proper citation: CRISPRcasIdentifier (RRID:SCR_018296) Copy   

•   Source: SciCrunch Registry

https://satijalab.org/howmanycells

Web tool for calculating number of cells that must be sampled in order to see at least n cells of each type for single cell genomics experiments.

Proper citation: How many cells (RRID:SCR_018184) Copy   

•   Source: SciCrunch Registry

http://www.innovision-systems.com/Products/MaxTraq.html

Software package for motion capture analysis by Innovision Systems Inc.

Proper citation: MaxTRAQ (RRID:SCR_018188) Copy   

•   Source: SciCrunch Registry

http://crispr.dbcls.jp/

Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast.

Proper citation: CRISPRdirect (RRID:SCR_018186) Copy   

•   Source: SciCrunch Registry

https://crowdfightcovid19.org/

Initiative from scientific community to put all available resources including highly skilled scientists at service of fight against COVID-19.

Proper citation: Crowdfight COVID-19 (RRID:SCR_018340) Copy   

•   Source: SciCrunch Registry

https://femtonics.eu/products/

Software package for measurement control and analysis by Femtonics Ltd. Designed in MATLAB and used in field of cellular and network imaging. New version offers new scanning features and improved overall usability.

Proper citation: Measurement Control And Data Analysis Software (RRID:SCR_018309) Copy   

•   Source: SciCrunch Registry

http://viewer.shigen.info/medakavw/crisprtool/

Web medaka pattern match tool for short sequence and/or pattern. Used to search database of medaka genome on target and off target sites when editing genome with CRISRP-Cas9.

Proper citation: NBRP Medaka Pattern Match (RRID:SCR_018157) Copy   

•   Source: SciCrunch Registry

https://www.becker-hickl.com/products/spcm/

Software tool as instrument software for SPC- and DPC Modules by Becker and Hickl GmbH.

Proper citation: SPCM (RRID:SCR_018310) Copy   

•   Source: SciCrunch Registry

http://statistika.mfub.bg.ac.rs/interactive-dotplot/

Web-based tool to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of continuous variable across different study groups, visualization of subgroups or clusters of non-independent data. Web visualization tool for creating dot plots, box plots and violin plots for small sample size data sets.

Proper citation: Interactive Dotplot (RRID:SCR_018329) Copy   

•   Source: SciCrunch Registry

http://stmichaelshospitalresearch.ca/wp-content/uploads/2015/09/ZEN-Black-Quick-Guide.pdf

Software used to analyze images obtained from microscope. ZEN Black is software Zeiss uses to run their laser-based instruments.

Proper citation: Black Zen software (RRID:SCR_018163) Copy   

•   Source: SciCrunch Registry

https://outbreak.info/

Resource to aggregate all outbreak information into single location during outbreaks of emerging diseases, such as COVID-19.

Proper citation: outbreak.info (RRID:SCR_018282) Copy   

•   Source: SciCrunch Registry

https://nemoanalytics.org/

Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.

Proper citation: NeMO Analytics (RRID:SCR_018164) Copy   

•   Source: SciCrunch Registry

https://dice-database.org

Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis.

Proper citation: Database of Immune Cell Epigenomes (RRID:SCR_018259) Copy   

•   Source: SciCrunch Registry

http://www.prc.boun.edu.tr/appserv/prc/hingeprot/index.html

Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures.

Proper citation: HingeProt (RRID:SCR_018136) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/biolucida

Enables visualization, storage and sharing of large image data. Cloud based system by MBF Bioscience to help with data from 2D and 3D slide scanners, confocal Z-stacks, lightsheet whole brain images. System for data storage and management, data analysis and visualization. Data is stored in secure and permanent way. Available also is free application named Biolucida Viewer, for viewing public images or images shared by collaborators owning Biolucida.

Proper citation: Biolucida (RRID:SCR_018256) Copy   

•   Source: SciCrunch Registry

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

Software R package for simultaneous inference in general parametric models. Offers interface to perform multiple comparisons in general context. Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models.

Proper citation: multcomp (RRID:SCR_018255) Copy   

•   Source: SciCrunch Registry

https://seaborn.pydata.org/

Software Python tool as data visualization library based on matplotlib. Provides interface for drawing attractive and informative statistical graphics. Statistical data visualization using matplotlib.

Proper citation: seaborn (RRID:SCR_018132) Copy   

•   Source: SciCrunch Registry