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https://github.com/hall-lab/bamkit
Software tools for common BAM file manipulations.
Proper citation: bamkit (RRID:SCR_023969) Copy
https://github.com/y-256/libdivsufsort
Software library that implements lightweight suffix array construction algorithm. Provides C API to construct suffix array and Burrows-Wheeler transformed string from given string over constant size alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of the string.
Proper citation: libdivsufsort (RRID:SCR_024079) Copy
https://github.com/lh3/miniasm
Software OLC-based de novo assembler for noisy long reads.
Proper citation: Miniasm (RRID:SCR_024114) Copy
http://libdisorder.freshdefense.net/
Software C library for entropy measurement of byte streams and other data.
Proper citation: libdisorder (RRID:SCR_024072) Copy
https://metacpan.org/dist/FAST
Software Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records.FAST workflows are designed for serial processing of flatfile biological sequence record databases per-sequence, rather than per-line, through UNIX pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FASTQ format is supported. FAST is designed for learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, and reproducibility. FAST tools expose the power of Perl and BioPerl to users in an easy-to-learn command-line paradigm.
Proper citation: FAST Analysis of Sequences Toolbox (RRID:SCR_024074) Copy
Software tool as general purpose cluster algorithm for both weighted and unweighted networks. Unsupervised cluster algorithm for graphs based on simulation of stochastic flow in graphs. Cluster algorithm for graphs.
Proper citation: MCL (RRID:SCR_024109) Copy
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://cran.r-project.org/package=RANN
Software R package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3).
Proper citation: rann (RRID:SCR_024297) Copy
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
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
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
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
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
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