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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://github.com/FePhyFoFum/phyx

Software phylogenetic tools for unix. Used to perform phylogenetics analyses on trees and sequences. Collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects.

Proper citation: Phyx (RRID:SCR_024164) 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://plastimatch.org/

Open source software for image computation with main focus on high performance volumetric registration, segmentation, and image processing of volumetric medical images.

Proper citation: Plastimatch (RRID:SCR_024168) Copy   

•   Source: SciCrunch Registry
  

https://pngquant.org/

Software command line utility and library for lossy compression of PNG images. The conversion reduces file sizes significantly and preserves full alpha transparency. Generated images are compatible with all web browsers and operating systems.

Proper citation: pngquant (RRID:SCR_024169) 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
  

https://github.com/BIMSBbioinfo/pigx_rnaseq

Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables.

Proper citation: PiGx-RNAseq (RRID:SCR_024160) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for clinical trial simulations based on Clinical Scenario Evaluation approach. The package supports broad class of data models, analysis strategies and commonly used evaluation criteria.

Proper citation: mediana (RRID:SCR_024281) Copy   

•   Source: SciCrunch Registry
  

https://github.com/scottgigante/picopore

Software tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality.

Proper citation: picopore (RRID:SCR_024161) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for creating iterators, many patterned after functions in the Python itertools module, and others patterned after functions in the 'snow' package.

Proper citation: itertools (RRID:SCR_024282) Copy   

•   Source: SciCrunch Registry