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revComp[1] = 2; //symbols[1]^rc = symbols[2] revComp[2] = 1; //symbols[2]^rc = symbols[1]

data[1] = new Sample( new DNASample( args[1] ), length );

...[http://www.oracle.com/technetwork/java/javase/downloads/index.html Java] 1.7 or later. {| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-al

Hausanschrift: von-Seckendorff-Platz 1, 06120 Halle, Germany<br />

data[1] = new Sample( new DNASample( args[1] ), length ); 1,

return x[0]*x[0] + x[1]*x[1]; return new double[]{2.0*x[0], 2.0*x[1]};

...hopped into overlapping k-mers, where k to the desired maximal PCT depth + 1. The PCT is learned on these resulting k-mers with the convention that the <td>1</td>

* '''Q₁: Why does the sampling create files in temporary directory of Java?'' * '''A₁:''' These files are created for saving the sampled parameter temporar

...ion centered at the position specified by the position tag, valid range = [1.0, 10000.0], default = 75.0)</td> ...ing factor (The value for weighting the data; either a value between 0 and 1, or a description relative to the standard deviation (e.g. +4sd), default =

1. We build a classifier that returns the probability that a specific cell fr ...MSP) learning principle and a product normal prior with standard deviation 1;

...ion centered at the position specified by the position tag, valid range = [1.0, 10000.0], default = 75.0)</td> ...ing factor (The value for weighting the data; either a value between 0 and 1, or a description relative to the standard deviation (e.g. +4sd), default =

...rameterSet(con,10,(byte)10,1E-9,1E-10,1, false,KindOfParameter.PLUGIN,true,1);

* [http://www.jstacs.de/downloads/EpiTALE-0.1.jar Runnable Jar]: requires Java >= 8 including JavaFX installed, may be r * [http://www.jstacs.de/downloads/EpiTALE-0.1.app.zip macOS app]: ZIP archive containing a macOS app including EpiTALE an

revComp[1] = 2; //symbols[1]^rc = symbols[2] revComp[2] = 1; //symbols[2]^rc = symbols[1]

* Dispom can be downloaded [http://www.jstacs.de/download.php?which=Dispom1.1 here]. <td>the sd of the a priori TFBS distribution, valid range = [1.0, Infinity], default = 150.0</td>

...gnment. In this example, we restrict to simple costs that are 0 for match, 1 for match, 0.5 for a gap. Costs costs = new SimpleCosts( 0, 1, 0.5 );

...determining the prediction threshold, valid range = [0.0, 0.01], default = 1.0E-4)</td> ...ted binding sites for determining the prediction threshold, valid range = [1, 1000000], default = 10000)</td>

{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-al ...ww.jstacs.de/downloads/workshop/jstacs-1.5.pdf '''''New Features of Jstacs 1.5''''']

* [http://www.jstacs.de/downloads/MeDeMo-1.0.jar command line interface] version and ...stacs.de/downloads/MeDeMoGUI-1.0.jar JAR file] (requires installed Java >= 1.8 and JavaFX)

...new GenDisMixClassifierParameterSet( alphabet, 10, (byte) 10, 1E-6, 1E-9, 1, false, KindOfParameter.PLUGIN, true, 2 ); ...rinciple. If we like to do so, we have to provide a weighting that sums to 1 and represents the weights for the conditional likelihood, the likelihood a

...If your parameterization is known to be convex, this method should return 1. ...d called <code>getProbFor(sequence.getSubSequence(startpos,endpos-startpos+1))</code>.

TALgetter is part if Jstacs release 2.1. You find the TALgetter sources in package <code>projects.tals</code>. ...ue of 0 or 1 switches off the filter., valid range = [0.0, 1.0], default = 1.0)</td>

...dium (q=0.4), Medium-Strict (q=0.45), Strict (q=0.5), valid range = [0.35, 1.0], default = 0.4)</td> ...rted targets in all input sequences, ranked by their score, valid range = [1, 100000], default = 100)</td>

...ericComplementableDiscreteAlphabet( true, new String[]{"A","B"}, new int[]{1,0} ); ...uot;) by setting the <math>0</math>-th value of the integer array to <math>1</math>.

* [http://www.jstacs.de/downloads/Catchitt-0.1.4.jar JAR download] ...f cell type-specific transcription factor binding]. ''Genome Biology'', 20(1):9, 2019.

.../jstacs/data/bioJava/BioJavaAdapter.html BioJavaAdapter] ported to BioJava 1.9 == Jstacs 2.1 (''released Mai 31, 2013'')==

java -jar GeMoMa-1.9.jar CLI GeMoMaPipeline ...ght that can be used in the filter, valid range = [0.0, 1000.0], default = 1.0, OPTIONAL)</td>

...h (The length of the seed at the 3' end of the protospacer, valid range = [1, 13], default = 12)</td>

java -jar GeMoMa-1.9.jar CLI GeMoMaPipeline threads=<threads> outdir=<outdir> GeMoMa.Score=ReA ...script prediction can be altered using the parameter "tag". Before version 1.7 the default value of tag was "prediction" instead of "mRNA".

..., "The required length of a sequence", true, new NumberValidator<Integer>( 1, 100 ), 10 );