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Component-based data mining and machine learning software suite written in C++, featuring a visual programming front-end for exploratory data analysis and interactive visualization, and Python bindings and libraries for scripting Linux, macOS, Windows: GPL: University of Ljubljana: SAMtools
RefSeq Functional Elements (RefSeqFE): It is focused on describing non-genic functional elements which are gene regulatory regions such as: enhancers, silencers, DNase I hypersensitive regions, DNA replication origins etc.). The current scope of this project is restricted to the human and mouse genomes.
queryable-rna-seq-database Formally known as the Queryable RNA-Seq Database, this system is designed to simplify the process of RNA-seq analysis by providing the ability upload the result data from RNA-Seq analysis into a database, store it, and query it in many different ways.
However, nearly all software meeting the Free Software Definition also meets the Open Source Definition and vice versa. A small fraction of the software that meets either definition is listed here. Some of the open-source applications are also the basis of commercial products, shown in the List of commercial open-source applications and services.
Python Package Index (formerly the Python Cheese Shop) is the official directory of Python software libraries and modules; Useful Modules in the Python.org wiki; Organizations Using Python – a list of projects that make use of Python; Python.org editors – Multi-platform table of various Python editors
It is an open-source cross-platform integrated development environment (IDE) for scientific programming in the Python language.Spyder integrates with a number of prominent packages in the scientific Python stack, including NumPy, SciPy, Matplotlib, pandas, IPython, SymPy and Cython, as well as other open-source software.
Slider is an application for the Illumina Sequence Analyzer output that uses the "probability" files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. Yes Yes No No [53] [54] 2009-2010 SOAP, SOAP2, SOAP3, SOAP3-dp SOAP: robust with a small (1-3) number of gaps and mismatches.
Since 7 October 2024, Python 3.13 is the latest stable release, and it and, for few more months, 3.12 are the only releases with active support including for bug fixes (as opposed to just for security) and Python 3.9, [55] is the oldest supported version of Python (albeit in the 'security support' phase), due to Python 3.8 reaching end-of-life.