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Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.
Proper citation: Debian (RRID:SCR_006638) Copy
Ratings or validation data are available for this resource
Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note.
Proper citation: neurodebian (RRID:SCR_004401) Copy
Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).
Proper citation: FreeContact (RRID:SCR_016113) Copy
American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook.
Proper citation: Google (RRID:SCR_017097) Copy
http://cakesomatic.sourceforge.net/
A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.
Proper citation: Cake (RRID:SCR_002133) Copy
https://github.com/mpyatkov/sbars
Bioinformatics tool for searching different types of long repeats in sequences comparable by size with chromosomes.
Proper citation: SBARS (RRID:SCR_002371) Copy
http://www.bioconductor.org/packages/release/bioc/html/CAMERA.html
A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.
Proper citation: CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) Copy
http://droog.gs.washington.edu/polyphred/
Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.
Proper citation: PolyPhred (RRID:SCR_002337) Copy
http://cran.r-project.org/web/packages/isa2/
A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.
Proper citation: Iterative Signature Algorithm (RRID:SCR_002327) Copy
http://cran.r-project.org/web/packages/ExomeDepth/
Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Proper citation: ExomeDepth (RRID:SCR_002663) Copy
http://www.bioconductor.org/packages/devel/bioc/html/MethylAid.html
Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.
Proper citation: MethylAid (RRID:SCR_002659) Copy
http://kirchnerlab.github.io/libmgf/
A flex/bison-based C++ Mascot Generic Format (MGF) parser library.
Proper citation: libmgf (RRID:SCR_002664) Copy
https://github.com/rcanovas/libCSAM
Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file.
Proper citation: libCSAM (RRID:SCR_002766) Copy
Whole genome secondary analysis on Illumina sequencing platforms.
Proper citation: Isaac (RRID:SCR_012772) Copy
http://bioconductor.org/packages/release/bioc/html/lumi.html
Software that provides an integrated solution for the Illumina microarray data analysis.
Proper citation: lumi (RRID:SCR_012781) Copy
http://bioinf.comav.upv.es/ngs_backbone/index.html
A bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences.
Proper citation: Ngs backbone (RRID:SCR_012907) Copy
http://www.bioconductor.org/packages/release/bioc/html/rqubic.html
This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data.
Proper citation: rqubic (RRID:SCR_012869) Copy
http://bioconductor.org/packages/release/bioc/html/DiffBind.html
Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
Proper citation: DiffBind (RRID:SCR_012918) Copy
http://www.bioconductor.org/packages/release/bioc/html/eisa.html
A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data.
Proper citation: eisa (RRID:SCR_012883) Copy
http://sourceforge.net/projects/trowel-ec/
An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.
Proper citation: Trowel (RRID:SCR_012890) Copy
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