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https://cran.r-project.org/package=stringi
Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing.
Proper citation: stringi (RRID:SCR_024319) Copy
Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments.
Proper citation: VARNA (RRID:SCR_024373) Copy
https://github.com/vgteam/vg#vg
Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes.
Proper citation: variation graph (RRID:SCR_024369) Copy
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
https://sourceforge.net/projects/trinculo/
Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping.
Proper citation: Trinculo (RRID:SCR_024384) Copy
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
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
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
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
Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias.
Proper citation: umis (RRID:SCR_024381) Copy
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
https://github.com/ncbi/sra-tools/
Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces.
Proper citation: sra-toolkit (RRID:SCR_024350) Copy
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
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
https://www.mathworks.com/products/optimization.html
Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations.
Proper citation: Optimization Toolbox (RRID:SCR_024486) Copy
https://github.com/danbider/lightning-pose
Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools.
Proper citation: Lightning Pose (RRID:SCR_024480) 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
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