Search Results for "reference" - Page 2
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Showing 43 open source projects for "reference"
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HSRA
Hadoop spliced read aligner for RNA-seq data
HSRA is a MapReduce-based parallel tool for mapping reads from RNA sequencing (RNA-seq) experiments. RNA-seq analyses typically begin by mapping reads to a reference genome in order to determine the location from which the reads were originated, which is a very time-consuming step. This tool allows bioinformatics researchers to efficiently distribute their mapping tasks over the nodes of a cluster by combining a fast multithreaded spliced aligner (HISAT2) with Apache Hadoop, which is a distributed computing framework for scalable Big Data processing. ... -
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sf (Simple Features)
Simple Features for R
...It allows spatial vector data (points, lines, polygons etc.) to be represented as records in data frames (or tibbles) with geometry list columns, and performs spatial operations (geometry operations, coordinate reference system transformations, reading/writing spatial data, integration with spatial databases etc.). It interfaces to GDAL, GEOS, PROJ libraries for robust operations. Reading and writing spatial vector data via many file formats/drivers through GDAL, and spatial databases (PostGIS etc.) Supports all standard simple feature geometry types (points, linestrings, polygons, multi-geometries etc.) in various dimensions (XY, XYZ, XYM, XYZM). -
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ParTools
Support for manual parallelization of sequential C programs.
ParTools allows the interactive analysis of a C program execution profile and data dependencies to facilitate the discovery and selection of suitable parallelization candidates in a manual parallelization process. The flow does not assume any specific parallelization technique, thus it can be broadly applied. The original (serial) C source is automatically annotated to trace the execution profile and data dependencies at run-time. The annotated program is then executed using a... -
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Taurus
A python based User Interface library.
The Taurus Project has *moved* to: https://github.com/taurus-org/taurus This SourceForge page is *outdated* and kept for historical reference only. Taurus is a python framework for control and data acquisition CLIs and GUIs in scientific/industrial environments. It supports multiple control systems or data sources: Tango, EPICS, ... New control system libraries and data sources can be integrated through plugins. -
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Informatica Create ctl
automate Informatica control file creation
...Default settings for the control file can be overridden at the command line and works with both static and dynamic deployment groups in the repository. Please review the “Using the Deployment Control File” section in the Informatica Command Reference guide for further help on the deployment control file. This utility supports Informatica PowerCenter versions 8.6.1 onwards and Java 1.6\. This utility also contains JDBC drivers for DB2, SQL Server, Oracle, and Teradata databases. -
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PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. PRADA currently supports 7 modules to process and identify... -
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Graphical Grammar Studio
An user friendly grammar tool for natural language processing tasks
...GGS grammars can be used to find and annotate sequences of words which respect certain conditions, in a given input. Its purpose is for creating NLP tools like phrase chunkers, named entity finders, pronoun co-reference solvers etc. A grammar is represented by a state machine which can be visualized, edited and applied. A grammar is organized in graphs of nodes. Nodes are used for consuming words from the input, for executing jumps to other graphs in the grammar or for creating annotations etc. GGS has a unique feature: It allows the user to write JavaScript code to be executed for nodes of the grammar. ... -
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CAPLET
GDS visualization and parallelized capacitance extraction
Project CAPLET is a capacitance extraction toolkit that extract capacitance at field-solver accuracy. CAPLET can directly handle GDS2 layout files into capacitance matrices in both GUI and command line interfaces. The internal extraction algorithm is specialized for VLSI interconnect structures but not exclusively, as long as the structure is of Manhattan geometry and embedded in a uniform dielectric material. -
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RenderTools
A cross-platform OpenGL based lightweight scenegraph library
RenderTools is an OpenGL based scenegraph library in C++ for Windows, OSX and IOS supporting OpenGL|ES1.1, ES2.0, OpenGL1.5 and up to the latest version (currently 4.2). It allows the developer to easily (de)serialize a scenegraph to-and-from xml, create renderbuffers, framebuffers, samplers, vertexbuffers etc. and cross-reference those items. RenderTools allows you to completely specify an application, its resources, viewcontrollers and its renderpasses in one single xml. GraphNodes such as RelationalNode, RenderNode, and TransformNode can be used to create a complex hierarchy for rendering. Both update and render calls can selectively include or exclude specific components such as geometric details or lighting or texturing. -
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SciPlore MindMapping is based on FreeMind but extended with features for students & researchers. It integrates mind maps with reference and pdf management (BibTeX support & PDF Bookmark import). Keywords: Mind maps, Mind Mapping, MindMap, JabRef
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UniCode C++ library, a replacement for libunicode. This library allows to use / create multiple code pages, convert to HTML, using the latest UniCode version as reference. Max flexibility and re-usability. Cross-platform applications published: xpfweb
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Quick reference for switching between mathematical computation environments for computer algebra, numeric processing and data visualisation. Examples are Matlab, IDL, SPlus, and their open-source counterparts Octave, Scilab, Python+NumPy and R.
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Eidola is a representation-independent programming language. This project supports the language core, including the semantics and the reference implementation of a kernel. See http://eidola.org/ for for information.
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ADrillForce project is now part (a component) of the larger project forssim. This project will close. ADrillForce is a reference implementation of haptic (force feedback) algorithms for virutal hard material collision handling and data modification.
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The aDORe Federation is a standards-based federated repository framework and reference implementation which aims to address many of the scalability issues experienced by large scale digital object repositories.
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TABSAT
Analysis Tool for Targeted Amplicon Bisulfite Sequencing
TABSAT - Targeted Amplicon Bisulfite Sequencing Analysis Tool A tool for analyzing targeted bisulfite sequencing data generated on an Ion Torrent PGM / Illumina MiSeq. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. Results are aggregated across all samples, presented in table format, and visualized as lollipop plots. In addition, due to the long read length of Ion Torrent reads, the pipeline is able to deduce specific methylation-patterns present in a sample. Please check out the Github page: https://github.com/tadkeys/tabsat
