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https://github.com/BIC-MNI/libminc
Software core library and API of the Medical Image NetCDF toolkit.
Proper citation: libminc (RRID:SCR_024086) Copy
https://github.com/rcsb/mmtf-python
Software Python implementation of MacroMolecular Transmission Format API, decoder and encoder. Repository holds the Python 2 and 3 compatible API, encoding and decoding libraries.
Proper citation: mmtf-python (RRID:SCR_024120) Copy
https://github.com/kdm9/libqcpp
Software C++11 library for next-gen sequence quality control and assessment.
Proper citation: libqc++ (RRID:SCR_024088) Copy
https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
SIMD Smith-Waterman C/C++ library for use in genomic applications. SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages.
Proper citation: SSW Library (RRID:SCR_024089) Copy
https://metacpan.org/dist/Bio-PrimerDesigner
Software package provides low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio-PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported.
Proper citation: Bio-PrimerDesigner (RRID:SCR_024082) Copy
https://svi-opensource.github.io/libics/
Software reference library for Image Cytometry Standard, an open standard for writing images of any dimensionality and data type to file, together with associated information regarding the recording equipment or recorded subject.Image Cytometry Standard file reading and writing.
Proper citation: libics (RRID:SCR_024085) Copy
https://sourceforge.net/projects/placnet/
Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools.
Proper citation: Placnet (RRID:SCR_024176) Copy
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
https://sourceforge.net/projects/poamsa/
Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment.
Proper citation: POA (RRID:SCR_024172) Copy
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
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
Software package for molecular graphics visualisation.Used for visualisation of molecules.
Proper citation: rasmol (RRID:SCR_024208) Copy
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
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
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
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
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
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
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
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
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