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

Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.

Proper citation: wavethresh (RRID:SCR_024311) Copy   

•   Source: SciCrunch Registry

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

Software R package to support gene set enrichment analysis, network topology analysis.Can be integrated into other pipeline or simultaneously analyze multiple gene lists. The user-friendly output report allows interactive and efficient exploration of enrichment results.

Proper citation: webgestaltr (RRID:SCR_024312) Copy   

•   Source: SciCrunch Registry

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

Software R package as collection of plotting and table output functions for data visualization. Results of various statistical analyses that are commonly used in social sciences can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, generalized linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models including interaction terms. This package supports labelled data.

Proper citation: sjplot (RRID:SCR_024307) Copy   

•   Source: SciCrunch Registry

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

Software R package for basic wavelet routines for time series 1D, image 2D and array 3D analysis.

Proper citation: waveslim (RRID:SCR_024308) Copy   

•   Source: SciCrunch Registry

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

Software R package provides framework to perform Non-negative Matrix Factorization.Used for nonnegative matrix factorization.Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.

Proper citation: nmf (RRID:SCR_024284) Copy   

•   Source: SciCrunch Registry

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

Software R tools for visualizing, smoothing and comparing receiver operating characteristic. Partial area under curve AUC can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.

Proper citation: proc (RRID:SCR_024286) Copy   

•   Source: SciCrunch Registry

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

Software R package useful in analyzing data from psychophysical experiments.Includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice data to be used with binomial family in glm and self-Start functions for estimating gamma values for CRT screen calibrations.

Proper citation: psyphy (RRID:SCR_024289) Copy   

•   Source: SciCrunch Registry

https://bioruby.org/

Software tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.

Proper citation: ruby-bio (RRID:SCR_024322) Copy   

•   Source: SciCrunch Registry

https://github.com/ggonnella/rgfa

Ruby library for handling GFA files.

Proper citation: rgfa (RRID:SCR_024323) Copy   

•   Source: SciCrunch Registry

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

Software R package to compute optimal cutpoints for diagnostic tests or continuous markers.Used for selecting optimal cutoffs, analysis and diagnostic test accuracy measures.

Proper citation: optimalcutpoints (RRID:SCR_024283) Copy   

•   Source: SciCrunch Registry

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

Software R package for design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints.

Proper citation: rpact (RRID:SCR_024300) Copy   

•   Source: SciCrunch Registry

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

Software R package provides computational framework for analyzing mutations in immunoglobulin sequences. Immunoglobulin Somatic Hypermutation Analysis.

Proper citation: shazam (RRID:SCR_024301) Copy   

•   Source: SciCrunch Registry

https://github.com/rrwick/Unicycler

Software assembly pipeline for bacterial genomes. Used for resolving bacterial genome assemblies from short and long sequencing reads. Can assemble Illumina only read sets where it functions as SPAdes-optimiser. Can assembly long read only sets for PacBio or Nanopore where it runs miniasm+Racon pipeline.

Proper citation: Unicycler (RRID:SCR_024380) Copy   

•   Source: SciCrunch Registry

https://github.com/dib-lab/sourmash

Software library for MinHash sketching of DNAsearch. Used to compare and analyze genomic and metagenomic data sets.

Proper citation: sourmash (RRID:SCR_024347) Copy   

•   Source: SciCrunch Registry

http://tab2mage.sourceforge.net/

Software package written and supported by ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets to our public repository database.

Proper citation: tab2mage (RRID:SCR_024359) Copy   

•   Source: SciCrunch Registry

http://www-personal.umich.edu/~jianghui/rseq/

A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations.

Proper citation: rSeq (RRID:SCR_000562) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/services/DictyOGlyc-1.1/

Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.

Proper citation: DictyOGlyc (RRID:SCR_001600) Copy   

•   Source: SciCrunch Registry

http://www.glycosciences.de/modeling/glyprot/

Web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II, http://www.glycosciences.de/modeling/sweet2/doc/index.php

Proper citation: GlyProt (RRID:SCR_001560) Copy   

•   Source: SciCrunch Registry

http://phospho.elm.eu.org/

Database of experimentally verified phosphorylation sites in eukaryotic proteins. Entries are manually curated with links to literature references, information about structure, interaction partners and sub-cellular compartment tissues, and sequences from the UniProt database.

Proper citation: Phospho.ELM (RRID:SCR_001109) Copy   

•   Source: SciCrunch Registry

http://hipipe.ncgm.sinica.edu.tw/

Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task.

Proper citation: HiPipe (RRID:SCR_001215) Copy   

•   Source: SciCrunch Registry