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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=survivalROC
Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data.
Proper citation: survivalROC (RRID:SCR_024415) 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
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://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/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
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
Data analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast.
Proper citation: BLASTP (RRID:SCR_001010) Copy
http://www.drive5.com/muscle/prefab.htm
Downloadable data designed for testing multiple sequence alignment methods.
Proper citation: PREFAB (RRID:SCR_001009) Copy
https://prosite.expasy.org/scanprosite/
Web tool for detecting PROSITE signature matches in protein sequences.
Proper citation: ScanProsite (RRID:SCR_024425) Copy
https://github.com/PyWavelets/pywt
Software Python package for wavelet analysis.
Proper citation: PyWavelets (RRID:SCR_024421) Copy
https://sciex.com/products/software/proteinpilot-software
Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems.
Proper citation: ProteinPilot (RRID:SCR_024414) Copy
https://github.com/paulgeeleher/pRRophetic
Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data,
Proper citation: pRRophetic (RRID:SCR_024417) Copy
https://github.com/torognes/vsearch
Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data.
Proper citation: VSEARCH (RRID:SCR_024494) Copy
https://www.tomocube.com/product/tomostudio/
Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data.
Proper citation: TomoStudio (RRID:SCR_024498) Copy
https://www.photometrics.com/products/ocular
Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system.
Proper citation: Ocular (RRID:SCR_024490) Copy
https://github.com/SharonLutz/Umediation
Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding.
Proper citation: Umediation (RRID:SCR_024492) Copy
https://www.reading.ac.uk/bioinf/IntFOLD/
Web integrated protein structure and function prediction server. Integrated server for modelling protein structures and functions from amino acid sequences.
Proper citation: IntFOLD (RRID:SCR_024523) Copy
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