Search Results for "tools"
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126 projects for "tools" with 2 filters applied:
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SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools
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BBMap
BBMap short read aligner, and other bioinformatic tools.
This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. ... -
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Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format. -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
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AMBIT:Chemical Structure DB&Web Service
Chemical structures database & machine learning with web services API
...Flexible structure, similarity and study queries storage, descriptor calculation and predictive models building via REST web services.User interface for creating read across assessment and generating reports, aligned with regulatory and industrial requirements. Command line applications also available. Integration with third party tools and databases. -
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Stanford Data Miner
Tools for integration and analysis of heterogeneous immunological data
An extensive description of this system is published in the Journal of Translational Medicine (http://www.translational-medicine.com/). In brief, the system consists of two main web applications, a data integration app and a data exploration app. The data integration app is a fully custom Java "Web 2.0" product called Sherpa. Sherpa uses Seam, a platform integrating Asynchronous JavaScript and XML (AJAX), JavaServer Faces (JSF), the Java Persistence API (JPA), and Enterprise Java Beans... -
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not... -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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This project hosts a library and tools for sharing simulation experiments encoded using SED-ML.
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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++. Our source code and wiki lives on GitHub (https://github.com/OpenMS/OpenMS).
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The Elvira project is a suite of tools to perform high-throughput genomic assemblies of repetitive, structured samples such as viruses or targeted regions of larger genomes.
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The ChIP-Seq software provides methods for the analysis of ChIP-seq data and other types of mass genome annotation data. The most common analysis tasks include positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-depleted regions.
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Genobuntu
Genobuntu Package for Next Generation Sequencing
Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting. ... -
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ProteoWizard development moved to GitHub in 2018. The ProteoWizard Library is a set of software libraries and tools for rapid development of proteomics data analysis software. The libraries are cross-platform and built from the ground up using modern C++ techniques.
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Collaborative Computing Project for NMR
Collaborative Computing Project for NMR (CCPN)
The Collaborative Computational Project for NMR (CCPN) provides tools and knowledge to maximise the impact of the biological NMR studies. The CCPN software facilitates data analysis and software integration. The project actively promotes the exchange of knowledge and provides training and best practices for the NMR community. CCPN also has a leading role in the development of a NMR data-sharing standard and coordination of NMR instrumentation proposals for RCUK and BIS. -
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...It deals with "hits" (predicted features) on biological sequences (protein, DNA), handles incremental updates effectively, supports taxonomy, and provides original query tools.
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RoadRunner represents a state-of-the-art simulation library for SBML models. It is fast, portable and accurate. This projects hosts the library and tools using the library.
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...More specifically, our software implements pipelines for the analysis of single nucleotide and copy-number variation, bisulfite-seq and ChIP-seq experiments using well-established tools to perform these common tasks. RUbioSeq+ is free and includes all the core functionalities implemented in the original release of RUbioSeq (v3.2.1) but, also, outperforms and expands RUbioSeq capabilities supporting the parallelized analysis of full genomes in computing farms. RUbioSeq+ also incorporates a new GUI designed for interdisciplinary research groups where bioinformaticians and biomedical researchers work together.
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Placnet
Placnet project
Plasmid Constellation Network project. Placnet is a new tools for plasmid analysis in NGS projects. Placnet has been written in Perl. It's been 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. -
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Molecular Simulation Grid
Provides high performance computing power and state of the art tools
MoSGrid focuses on the configuration and provision of Grid services for molecular simulations and annotation of the results with metadata and their provision for data mining and knowledge generation. It is based on Liferay technology togethe with gUSE. -
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Krona
Hierarchical data browser
Krona allows hierarchical data to be explored with zoomable HTML5 pie charts. Krona charts can be created using an Excel template or Krona Tools, which includes support for several bioinformatics tools and raw data formats. -
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Suite of tools for DNA sequence analysis - searching (EST, mRNA, sequencer reads); aligning (ESTs, mRNA, whole genome); and analysis (repeats, kmers).
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GFinisher
genome assembler finisher, gap, gap close, sort contig
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. contact dievalg at gmail.com
