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https://CRAN.R-project.org/package=ggridges
Software R package enables creation of Ridgeline plots in 'ggplot2'
Proper citation: ggridges (RRID:SCR_024511) Copy
https://CRAN.R-project.org/package=gamm4
Software R package to estimate generalized additive mixed models.
Proper citation: gamm4 (RRID:SCR_024507) Copy
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
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
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
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
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
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
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
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
https://github.com/biod/sambamba
Software tools for working with SAM/BAM data
Proper citation: sambamba (RRID:SCR_024328) Copy
https://bioconductor.org/packages/release/bioc/html/annotate.html
Software R package for using R enviroments for annotation.
Proper citation: annotate (RRID:SCR_024221) Copy
https://gitlab.com/chrjan/seq-seq-pan
Software workflow for SEQuential alignment of SEQuences to build PAN-genome data structure and whole-genome-alignment.
Proper citation: seq-seq-pan (RRID:SCR_024343) Copy
https://bioconductor.org/packages/release/bioc/html/affyio.html
Software R package as routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing CEL and CDF file formats.
Proper citation: affyio (RRID:SCR_024223) Copy
https://github.com/losonczylab/sima
Software Python package for analysis of dynamic fluorescence microscopy data.
Proper citation: SIMA (RRID:SCR_024466) Copy
https://github.com/SciTools/cartopy
Software Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses. Cartographic library with matplotlib support.
Proper citation: Cartopy (RRID:SCR_024587) Copy
https://bioconductor.org/packages/release/bioc/html/altcdfenvs.html
Software R package contains convenience data structures and functions to handle cdfenvs.
Proper citation: altcdfenvs (RRID:SCR_024225) Copy
https://mc-stan.org/bayesplot/
Software R package providing extensive library of plotting functions for use after fitting Bayesian models.Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow.
Proper citation: bayesplot (RRID:SCR_024588) Copy
http://www.ncbi.nlm.nih.gov/medgen/
A database of organized information related to human medical genetics, such as attributes of conditions with a genetic contribution.
Proper citation: MedGen (RRID:SCR_000111) Copy
https://bioconductor.org/packages/microbiome/
Software R package for use in microbiome analysis. Used to provide comprehensive collection of tools and tutorials, with particular focus on amplicon sequencing data.
Proper citation: microbiome (RRID:SCR_024699) Copy
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