Search Results for "command line replacement" - Page 3
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Showing 478 open source projects for "command line replacement"
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mirplant
miRPlant: An Integrated Tool for Identification of Plant miRNA
please cite: An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275. We will create index for you if you tell us your interested plants (j.an@qut.edu.au). -
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Mavscript
Calculations in a text document
Mavscript allows the user to do calculations in a text document. Plain text, LaTeX and OpenOffice Writer files (.odt) are supported. The calculation is done by the algebra system Yacas (default), Jasymca or by the Java interpreter BeanShell. -
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PPICompare
detection of rewiring events in protein interaction networks
PPICompare detects statistically significant rewiring events in protein-protein interaction networks - even if they are caused by alternative splicing - and reports plenty of information to that. The input data needs to be constructed with PPIXpress (see https://sourceforge.net/projects/ppixpress/). The original publication can be found on https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0400-x. -
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Java G-Code Utils
Utilities for CNC (G-Code) using Java
Utilities for CNC (G-Code) using Java -
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As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the...
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Mapyrus is software to plot Geographic Information System data to PostScript, PDF, SVG and web image files. Mapyrus combines a BASIC-like scripting language, reading GIS datasets and running as either a utility program, a Java Servlet, or as a webser
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The Teachingbox uses advanced machine learning techniques to relieve developers from the programming of hand-crafted sophisticated behaviors of autonomous agents (such as robots, game players etc...) In the current status we have implemented a well founded reinforcement learning core in Java with many popular usecases, environments, policies and learners. Obtaining the teachingbox: FOR USERS: If you want to download the latest releases, please visit:...
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GLPK for Windows
Windows binaries for the GNU Linear Programming Kit (GLPK)
GLPK 4.65 (GNU Linear Programming Kit, http://www.gnu.org/software/glpk/) is a solver for large-scale linear programming (LP), and mixed integer programming (MIP). This project supplies the most recent Windows executables - 2018-03-17. Linux and OSX users should download the source distribution from http://ftp.gnu.org/gnu/glpk -
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JPIV
Particle Image Velocimetry
JPIV is a platform independent, graphical stand-alone application for Particle Image Velocimetry (PIV) written in Java. PIV is an optical technique for measuring fluid flow velocities. JPIV moved to GitHub. Please visit us at: https://eguvep.github.io/jpiv/ -
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BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other... -
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Latin Square Toolbox
Generates Latin squares and counts their transversals
The Latin Square Toolbox contains software tools for efficiently generating Latin squares and counting their transversals with various user-configurable options. This open source release aims to help educate folks on Latin squares and their important applications to cryptography. This version contains three tools: 0. Latin Square Generator (LSG) 1. Latin Square Transversal Counter (LSTC) 2. Latin Square Property Checker (LSPC) -
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CRUSH
Data reduction and imaging for select astronomical cameras
CRUSH is a pioneering reduction and imaging suite for many astronomical cameras operating at far-infrared, submillimeter and millimeter wavelengths, such as SHARC-2, SCUBA-2, LABOCA, GISMO, or SOFIA/HAWC+ (to name a few). -
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The Helsinki Finite-State Transducer toolkit is intended for processing natural language morphologies. The toolkit is demonstrated by wide-coverage implementations of a number of languages of varying morphological complexity.
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spectralHMM
A spectral method for inferring selection from time series data
***WARNING*** This software was migrated to: https://github.com/popgenmethods/spectralHMM Support and updates will only be available at this new address. This software implements the algorithms described in the following paper: Steinrücken, M., Bhaskar, A. and Song, Y.S. A novel spectral method for inferring general diploid selection from time series genetic data. Annals of Applied Statistics, Vol. 8, No. 4 (2014) 2203-2222 -
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MYRA
A collection of ACO algorithms for the data mining classification task
MYRA is a collection of Ant Colony Optimization (ACO) algorithms for the data mining classification task. It includes popular rule induction and decision tree induction algorithms. The algorithms are ready to be used from the command line or can be easily called from your own Java code. They are build using a modular architecture, so they can be easily extended to incorporate different procedures and/or use different parameter values. This project is now hosted at: https://github.com/febo/myra -
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CSV Comparator
CSV Comparator is a tool for comparing files which contain CSV-Data.
...It was created for performance engineers to be able to have a easy way to compare data from two testruns and be able to automate the comparing process of various files with scripts. There is a command line tool as well as a user interface. In case you need to compare .xml-Files you can convert them to .csv-Files with my other project CSV Transformer. The advantages by using CSV as input and output are the following: - Many applications allow an export of its data to CSV or Excel(were it could be saved to CSV) - It is possible to pre- and postprocess the data, e.g removing version numbers before comparing - It is easy to create CSV data from logfiles and other resources by using unix tools like sed or awk - CSV can be loaded into other applications, especially Excel, were it can be formatted by macros for analyzing. -
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openmsr is a collection of tools around Instrumentation,Control and Automation ( ICA ). It runs under the following OS: Windows, Linux and Mac OSX. Ther are tools like digital simulation, object recognition, SoftPLC. Tools Messen,Steuern und Regeln
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The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.
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metawatt
Binner for assembled metagenomes
The Metawatt binner is a graphical binning tool that makes use of multivariate statistics of tetranucleotide frequencies and differential coverage based binning. It also performs taxonomic assessment of binning quality (via diamond BLASTx). Created bins can be edited and exported as fasta. The Metawatt is implemented in Java SWING and minimally depends on Diamond, HMMer3.1, BBMap, Prodigal and the Batik library for the export of SVG graphics. Citation: Strous M, Kraft B, Bisdorf R,... -
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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 -
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TER implements the CCSDS Recommendation for Image Data Compression (CCSDS 122.0-B-1). TER also adds new features to the Recommendation. TER is designed and programmed with the aim to provide a good basis to test and develop the CCSDS Recommendation.
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PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study).
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KAnalyze
DNA/RNA Sequence K-mer Toolkit
KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers. It is both a command line application and an API. -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
...The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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Opt4J
Modular Java framework for meta-heuristic optimization
Opt4J is an open source Java-based framework for evolutionary computation. It contains a set of (multi-objective) optimization algorithms such as evolutionary algorithms (including SPEA2 and NSGA2), differential evolution, particle swarm optimization, and simulated annealing. The benchmarks that are included comprise ZDT, DTLZ, WFG, and the knapsack problem. The goal of Opt4J is to simplify the evolutionary optimization of user-defined problems as well as the implementation of arbitrary...
