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https://cran.r-project.org/package=psychotree

Software R package for recursive partitioning based on psychometric models, employing general MOB algorithm to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models.

Proper citation: psychotree (RRID:SCR_024288) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/dynamicTreeCut/index.html

Software R package contains methods for detection of clusters in hierarchical clustering dendrograms.

Proper citation: dynamicTreeCut (RRID:SCR_024280) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/bedr/vignettes/Using-bedr.html

Software R package for genomic interval processing.Genomic regions processing using open-source command line tools to perform genome arithmetic e.g indexing, formatting and merging.

Proper citation: bedr (RRID:SCR_024526) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot.

Proper citation: ROCit (RRID:SCR_024420) Copy   

•   Source: SciCrunch Registry
  

https://zzz.bwh.harvard.edu/luna/

Software package for analysis of sleep signal data. Open source C/C++ software for manipulating and analyzing polysomnographic recordings, with focus on sleep EEG.

Proper citation: Luna (RRID:SCR_024541) Copy   

•   Source: SciCrunch Registry
  

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

Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats.

Proper citation: Rgdal (RRID:SCR_024422) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/package=Rwave

Software R package provides environment for Time-Frequency analysis of 1-D signals.

Proper citation: rwave (RRID:SCR_024302) Copy   

•   Source: SciCrunch Registry
  

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

Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data.

Proper citation: survivalROC (RRID:SCR_024415) 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
  

https://github.com/MMV-Lab/mmv_im2im

Software Python package for image to image transformation in bioimaging applications. Can be used for semantic segmentation, instance segmentation, image restoration, image generation, and more.

Proper citation: MMV Im2Im (RRID:SCR_024630) Copy   

•   Source: SciCrunch Registry
  

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

Software R package enables creation of Ridgeline plots in 'ggplot2'

Proper citation: ggridges (RRID:SCR_024511) Copy   

•   Source: SciCrunch Registry
  

https://CRAN.R-project.org/package=gamm4

Software R package to estimate generalized additive mixed models.

Proper citation: gamm4 (RRID:SCR_024507) 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
  

https://github.com/navinlabcode/copykat

Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data.

Proper citation: CopyKAT (RRID:SCR_024512) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for choosing univariate class intervals for mapping or other graphics purposes.

Proper citation: classInt (RRID:SCR_024515) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for multiple imputation of missing data in multilevel modeling.

Proper citation: mitml (RRID:SCR_024516) Copy   

•   Source: SciCrunch Registry
  

https://www.caida.org/

Center aimes at promoting greater cooperation in engineering and maintenance of global Internet infrastructure, better manage ever increasing volume of digitally based information including security and network data analysis. Provides open access data and tools.

Proper citation: SDSC Center for Applied Internet Data Analysis (RRID:SCR_024638) Copy   

•   Source: SciCrunch Registry
  

https://simpleitk.org/

Open source software library for multi dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++. New interface to Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. Provides easy to use and simplified interface to ITK's algorithms.

Proper citation: SimpleITK (RRID:SCR_024693) Copy   

•   Source: SciCrunch Registry
  

https://www.thermofisher.com/au/en/home/electron-microscopy/products/software-em-3d-vis/maps-software.html

Correlative electron microscopy and cross-platform imaging automation software. Imaging and correlative workflow software suite compatible with full line of Thermo Scientific SEM, DualBeam (FIB SEM) and TEM platforms.

Proper citation: Thermo Scientific Maps Software (RRID:SCR_024446) Copy   

•   Source: SciCrunch Registry
  

https://github.com/khowe/quicktree/

Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments.

Proper citation: quicktree (RRID:SCR_024205) Copy   

•   Source: SciCrunch Registry