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https://github.com/SouthGreenPlatform/rap-green
Software phylogenetic tree analysis package. Phylogenetic tree management, exploration and display package.
Proper citation: RapGreen (RRID:SCR_024426) 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://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
http://www.ncbi.nlm.nih.gov/tools/primer-blast/
A tool to design target-specific primers for polymerase chain reaction (PCR). It uses Primer3 to design PCR primers and then uses BLAST and global alignment algorithm to screen primers against user-selected database in order to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause non-specific amplifications.
Proper citation: Primer-BLAST (RRID:SCR_003095) Copy
https://github.com/blackrim/phyutility
Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI.
Proper citation: Phyutility (RRID:SCR_018545) Copy
https://sedfitsedphat.nibib.nih.gov/software/default.aspx
Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.
Proper citation: SEDFIT (RRID:SCR_018365) Copy
http://www.prisma-statement.org/
Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.
Proper citation: PRISMA (RRID:SCR_018721) Copy
http://bioinf.wehi.edu.au/software/elda/
Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly.
Proper citation: ELDA (RRID:SCR_018933) Copy
https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/
Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR.
Proper citation: PROCHECK (RRID:SCR_019043) Copy
http://www.biosoft.com/w/calcusyn.htm
Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools.
Proper citation: CalcuSyn (RRID:SCR_020251) Copy
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