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https://prinseq.sourceforge.net/

Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format.

Proper citation: PRINSEQ (RRID:SCR_024178) Copy   

•   Source: SciCrunch Registry

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

Software R package provides access to phyloinformatic data in 'NeXML' format.

Proper citation: rnexml (RRID:SCR_024291) Copy   

•   Source: SciCrunch Registry

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

Software R package provides base S4 class for comparative methods, incorporating one or more trees and trait data. Used for phylogenetic analysis.

Proper citation: phylobase (RRID:SCR_024292) Copy   

•   Source: SciCrunch Registry

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

Software R package to create Q-Q and manhattan plots for GWAS data from PLINK output files.

Proper citation: qqman (RRID:SCR_024293) Copy   

•   Source: SciCrunch Registry

https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index

Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures.

Proper citation: PLIP (RRID:SCR_024173) Copy   

•   Source: SciCrunch Registry

https://github.com/COMBINE-lab/RapMap

Software tool for mapping RNA-seq reads to transcriptomes. Used for rapid sensitive and accurate read mapping via quasi-mapping

Proper citation: rapmap (RRID:SCR_024204) Copy   

•   Source: SciCrunch Registry

http://rasmol.org/

Software package for molecular graphics visualisation.Used for visualisation of molecules.

Proper citation: rasmol (RRID:SCR_024208) Copy   

•   Source: SciCrunch Registry

https://github.com/silx-kit/pyFAI

Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments.

Proper citation: pyFAI (RRID:SCR_024186) Copy   

•   Source: SciCrunch Registry

http://www.bmsc.washington.edu/raster3d/raster3d.html

Software tools for generating high quality raster images of proteins or other molecules. Photorealistic molecular graphics. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing.

Proper citation: Raster3D (RRID:SCR_024220) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Biobase.html

Software R package provides functions that are needed by many other packages or which replace R functions. Base functions for Bioconductor.

Proper citation: Biobase (RRID:SCR_024224) Copy   

•   Source: SciCrunch Registry

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

Software R package to scrape data from Fitbit to generate graphs.

Proper citation: fitbitscraper (RRID:SCR_024273) Copy   

•   Source: SciCrunch Registry

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

Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data.

Proper citation: fitdistrplus (RRID:SCR_024274) Copy   

•   Source: SciCrunch Registry

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

Software R package for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.

Proper citation: forecast (RRID:SCR_024277) Copy   

•   Source: SciCrunch Registry

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

Software R package as implementation of LexRank algorithm. Used for computing sentence importance based on concept of eigenvector centrality in graph representation of sentences.

Proper citation: lexrankr (RRID:SCR_024278) Copy   

•   Source: SciCrunch Registry

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

Software R package for data objects in R to render as HTML tables using JavaScript library DataTables. DataTables library has been included in this R package.

Proper citation: DT (RRID:SCR_024270) 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://qtltools.github.io/qtltools/

Software tool set for molecular Quantitative Trait Loci discovery and analysis. Allows to go from raw sequence data to collection of molecular Quantitative Trait Loci in few easy-to-perform steps.

Proper citation: qtltools (RRID:SCR_024200) 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://gitlab.com/RKIBioinformaticsPipelines/QCumber

Software for quality control, quality trimming, adapter removal and sequence content check of NGS data.

Proper citation: qcumber (RRID:SCR_024203) Copy   

•   Source: SciCrunch Registry