sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d031bdd839f33299f807a673789ab911f1ee7841410e26676661d04eb2321343 | Java | 16,586 | 593 | package umcg.genetica.graphics.panels;
import umcg.genetica.containers.Pair;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import umcg.genetica.math.stats.Correlation;
import umcg.genetica.math.stats.Regression;
import umcg.genetica.util.Primitives;
import java.awt.*;
import java... |
6c362ebbf901307edd7bc7370c4c28b0b81c4c62fcefc702f2b97e6fc5f96cb0 | Java | 16,591 | 479 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
65231a5bee9a255221a883fd50c8fc6a2507b2e301b106805440be8421788b22 | Java | 16,611 | 607 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.gwascatalog;
import java.io.File;
import umcg.genetica.io.text.TextFile;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.u... |
19fecbaeed71c7cd08bebf3b53a1fc5f43b7b069c7727b5aaae0d45d58d98f8a | Java | 16,669 | 560 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
caac8d0b2c1c7d81fd2906125651d92ed37c1e285df2a036a09a79a8f35e267f | Java | 16,758 | 326 | package nl.systemsgenetics.geneticriskscorecalculator;
import gnu.trove.map.hash.TObjectDoubleHashMap;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Pattern;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.RandomAccessGenotypeData;
import org.molgenis.genotype.Alleles;
im... |
de781a571ccc46399069c96a15c557ad7e22802342908e2363acccc5b31e5e79 | Java | 16,761 | 449 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.util;
import java.util.*;
import java.util.stream.IntStream;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypeDataException;
... |
49807cb1a4ee03fc816383ac033320993854e10400edb378db31a0b317acb5d3 | Java | 16,815 | 624 | /* Copyright (c) 2019 Thomas Braschler <thomas.braschler@unige.ch>
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or
## (at your option) any later version... |
2d08e9034741c6fad952e9e05c4486526ef062e97d7da62646f386bbd01dd658 | Java | 16,929 | 380 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.io;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import java.io.File;
import java.io.FileNo... |
1aed518daa72687ea38b741d7f0614943416f34133956147bfd4e829c1fc1846 | Java | 17,061 | 470 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
91219f1982596e2f8761ff70f834d19ab76ee4b8189956d88d6b6caf599ba396 | Java | 17,144 | 449 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
f33b53c43f79c3cb63c73ad4b521a6bdf1d077187c6e6958414ae33a8a2c5591 | Java | 17,150 | 457 | /*-
* #%L
* Mavenized version of the BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code mus... |
51c1a7438abd16fb738fdca734631f444be263e0576a1133211e4056403101e6 | Java | 17,273 | 355 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.util.ArrayList;
import java.ut... |
d5a57db83798c22a2ec099faadf211bd0a00d20a88eee859089769dc7d2ea8f4 | Java | 17,288 | 421 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.simplegeneticriskscorecalculator;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import gnu.trove.map.hash... |
72b8c9ae83f36647a2a7103ba84f2ebee2820c3ae5fad733adfa6f027cd2ba4e | Java | 17,403 | 494 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may ... |
f6f6dd65887ef6c3a8f44e30d84f0eac687a020eb38f3279b99bbdd1a74822e0 | Java | 17,422 | 381 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.converters;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Set;
import java.util.regex.Matcher;
import java.util... |
8f57e29c4ffdac40654630dafc5a71ec578c0b5ca6e2a1b0519a2e3c9d1e516d | Java | 17,430 | 378 | package main.java.decon_eQTL;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import org.apache.commons.lang3.time.DurationFormatUtils;
import or... |
38db79e6c0e978a5735aebda24a9451ac7f6a776e1913998d617e098d483433d | Java | 17,440 | 483 | package eqtlmappingpipeline.binaryInteraction;
import au.com.bytecode.opencsv.CSVWriter;
import eqtlmappingpipeline.Main;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;... |
dc08b96db3df3869bf753956ff9c28c9199b5c8e8fd5091f709b8bc6ffd72cb3 | Java | 17,451 | 338 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.text.parsing;
import java.io.IOException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import umcg.genetica.io.text.TextFile;
/**
*
* @author juha
*/
public class Demographic... |
3da2d6f33345ae216bbc7a446b7d9e714ece0c9d8d1cf52f2cc553c0286dac2a | Java | 17,515 | 554 | package umcg.genetica.graphics.panels;
import umcg.genetica.containers.Pair;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import umcg.genetica.graphics.themes.DefaultTheme;
import umcg.genetica.graphics.themes.Theme;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.ma... |
6a28843880485dd7473a0c2d1047c7d14a684c7ff6cdfe6ef9c60e0f51da4f52 | Java | 17,519 | 550 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta;
import eqtlmappingpipeline.binarymeta.meta.graphics.ZScorePlot;
import umcg.genetica.io.trityper.EQTL;
import umcg.genetica.io.trityper.bin.BinaryResultDataset;
import umcg.g... |
767c27d417a8cd8419eb368505383bf9ec233523030a8c54c365a9b826b5dd38 | Java | 17,842 | 612 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
264ea9e014eec18b6e0ac6dcbe5dbe7e18130c4b2fd2c8868bea1fedd02d3a9e | Java | 17,911 | 484 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io... |
0d6fce42c0d5341f83399dc9d9f9aaecd3058da6194269c8fac978880e59da6f | Java | 17,913 | 520 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper;
import gnu.trove.map.hash.TObjectIntHashMap;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityp... |
72beb393074f5bfb9980f7f3d94e827b6be885b0f55bb5af8533b4481492fcaf | Java | 17,972 | 485 | package nl.systemsgenetics.genenetworkbackend.predictions;
import cern.jet.random.tdouble.StudentT;
import cern.jet.random.tdouble.engine.DRand;
import cern.jet.random.tdouble.engine.DoubleRandomEngine;
import cern.jet.stat.tdouble.Probability;
import gnu.trove.list.TDoubleList;
import gnu.trove.list.array.TDoubleArra... |
2d3270548abc8013dbd2d7d18ce018687de4bed72ce31f5e71f58ec14119b5ba | Java | 18,023 | 536 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the ... |
ffa986551cad6c2b31dcc401e52f3243a45605830d325ce5320f005080973b12 | Java | 18,202 | 423 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.gwas;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Ve... |
adfe3cc5aca93bc95c7422838141d2513df41b3fa4737b9fe9d44581137db546 | Java | 18,210 | 544 | /* * To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3;
import cern.colt.matrix.tint.IntMatrix2D;
import eqtlmappingpipeline.metaqtl3.containers.Settings;
import eqtlmappingpipeline.metaqtl3.containers.WorkPackage;
import umcg.genetica.i... |
ba57a6a2658551649742f6783fbb6451cf8bc2a56a15ada96639d1343906cb48 | Java | 18,220 | 515 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import au.com.bytecode.opencsv.CSVReader;
import au.com.bytecode.opencsv.CSVWriter;
import java.io.F... |
d6aebd9bb88791a913da5da5d65a87226571b8b57221e85d88ddcda48b5269de | Java | 18,256 | 454 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
7afa28ee839c9a4aaa18c488a9809d035b8722c0fc4de45682d19d79ed0c0ca6 | Java | 18,275 | 479 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
df602b0f9da190cd340ee952bd151952190d9f91a7d5d9d79f2f88f705109548 | Java | 18,277 | 507 | package nl.umcg.westrah.binarymetaanalyzer;
import gnu.trove.map.hash.TObjectIntHashMap;
import umcg.genetica.containers.Triple;
import umcg.genetica.io.trityper.util.BaseAnnot;
import umcg.genetica.math.stats.Descriptives;
import umcg.genetica.math.stats.ZScores;
import umcg.genetica.text.Strings;
import java.text.D... |
0640ff58b22920085284b80c1e71db7ccf67aad46a30caa37bbaec4804bdfabd | Java | 18,396 | 439 | package eqtlmappingpipeline.interactionMeta;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVReader;
import com.opencsv.CSVReaderBuilder;
import me.tongfei.progressbar.Prog... |
84d419c8f6a761f70cd7d0ea3af5082615a55db115ea926224ad0980428b21fc | Java | 18,527 | 626 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
697d8ced2481152856e82b28c28e857ecb6223184cf6d44a286dcac649e59291 | Java | 18,597 | 555 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.bondermj.microbialmetanalysis;
import gnu.trove.map.hash.TObjectIntHashMap;
import nl.umcg.westrah.binarymetaanalyzer.... |
7f1683ee892a1ad63a4eac2ea1afde9a519e170dce9931fd188524507779e375 | Java | 18,855 | 544 | /*
* SymmetricShortDistancaMatrix.java
*
* Created on 04 June 2004, 16:03
*/
package umcg.genetica.math.matrix;
/**
*
* Symmetric Short Distance Matrix: A memory efficient matrix capable of performing calculations on all genes x all genes:
*
* @author Lude Franke
*/
public class SymmetricShortDistanceMatrix... |
07e5f364d656d88f6a2850638b2c70636388b1f3b4754d48d3175fbb5a7237a8 | Java | 18,871 | 402 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.causalinference;
import eqtlmappingpipeline.metaqtl3.containers.Settings;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import u... |
f98a5039eac6d54b3f8b08501aa56a28e0056a8f6c736b9267a520f44c6175f7 | Java | 18,911 | 420 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.conditionalanalysis;
import eqtlmappingpipeline.metaqtl3.EQTLRegression;
import eqtlmappingpipeline.metaqtl3.FDR;
import eqtlmappingpipeline.metaqtl3.MetaQTL3;
import gnu.trove.set.h... |
42137c5b0fe2e158e57a84a8865b1b955fd78da258ce1ff4944bf748f30fc567 | Java | 18,919 | 406 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import umcg.genetica.containers.Pair;
import umcg.genetica.containers.SortableSNP;
import umcg.gene... |
6548df0e0fa8687faa5d97dd6fbd282f02fc9ab8b83a196a2ecc2e12da96d0aa | Java | 18,960 | 550 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import JSci.maths.ArrayMath;
import JSci.maths.statistics.NormalDistribution;
import java.io.IOException;
import java.util.Arrays;
import umcg.genetica.math.matrix.DoubleMatrixDataset;
... |
edbb9e8807a8071dadcf418f874ac1e9cff726757d375dda2b7889f9b9e63392 | Java | 18,963 | 662 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc.ld;
import org.apache.commons.math3.stat.correlation.PearsonsCorrelation;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.util.BaseAnnot;
import umcg.genetica.text.Strings;
import umcg.ge... |
8b11c724d24d94da8b8ac09d60f962e09bb4efcfa8386f0f6777069e3ab4923b | Java | 19,020 | 530 | package nl.systemsgenetics.downstreamer.io;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVReader;
import com.opencsv.CSVReaderBuilder;
import htsjdk.samtools.util.IntervalTreeMap;
import nl.systemsgenetics.downstreamer.DownstreamerDeprecated;
import nl.systemsgenetics.downstr... |
1601e3a4faba94395ae706efc16958a6087a8da158acf8a11037a8f1e2a0a16b | Java | 19,029 | 400 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.geofiles;
import java.io.*;
import java.util.*;
import java.util.regex.Pattern;
import umcg.genetica.math.matrix.DoubleMatrixDataset;
import umcg.genetica.methylation.SoftfileAnnotation;
/**
*... |
eeb097c9a0a330f08b09dcb345a14760829fc1748af8a63a7c10522510c8f31c | Java | 19,105 | 568 | package nl.systemsgenetics.genenetworkbackend.predictions;
import java.io.*;
import java.net.*;
import java.util.*;
import java.awt.image.BufferedImage;
import java.awt.image.*;
import java.awt.*;
import java.awt.geom.*;
import java.lang.Math;
import javax.imageio.*;
/**
*
* @author lude
*/
public class Expression... |
596eab8bd717d2f567b7dcb089601293cfd9df07c6ae692eef53230f01e7855d | Java | 19,186 | 536 | ///*
// * To change this template, choose Tools | Templates
// * and open the template in the editor.
// */
package eqtlmappingpipeline.binarymeta.meta;
//
//import eqtlmappingpipeline.gpio.binary.Dataset;
import eqtlmappingpipeline.binarymeta.meta.graphics.ZScorePlot;
import eqtlmappingpipeline.metaqtl3.FDR;
import e... |
45631cf5c6d9a4a1af2f49dfc2a28985f983a38e55b1b97c16a728927ee03a1a | Java | 19,194 | 615 | package umcg.genetica.graphics;
import com.itextpdf.text.DocumentException;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.features.Feature;
import umcg.genetica.features.FeatureComparator;
import umcg.genetica.features.GFFFile;
import umcg.genetica.graphics.themes.ComplementaryColor;
import umcg.genetica... |
a1db193ee319bc5baf4166ae3b723348f87176423d953a2beb415b9a846aec3e | Java | 19,301 | 547 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
881315379e8582d26864cbb0502d18a85a4d13542709b4722dd9a8b0cbcfd891 | Java | 19,393 | 455 | package mbqtl.junk;//package betaqtl.junk;
//
//import betaqtl.*;
//import betaqtl.vcf.VCFTabix;
//import betaqtl.vcf.VCFVariant;
//import umcg.genetica.console.ProgressBar;
//import umcg.genetica.containers.Triple;
//import umcg.genetica.enums.Chromosome;
//import umcg.genetica.features.Feature;
//import umcg.genetica... |
00346044a31f2ba45ff60992258eb90507ec50458c51ff5f2675c999774e7407 | Java | 19,424 | 498 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.graphics;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Graphics2D;
import java.awt.Polygon;
import java.awt.RenderingH... |
9485038d36985ad77ba75686d5681d56f2871f4349673df7e8857081a802c35c | Java | 19,439 | 491 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc.ld;
import nl.umcg.westrah.binarymetaanalyzer.BinaryMetaAnalysis;
import nl.umcg.westrah.binarymetaanalyzer.BinaryMetaAnalysisDataset;
import nl.umcg.westrah.binarymetaanalyzer.MetaQTL4MetaTrait;
import umcg.genetica.console.ProgressBar;
imp... |
d4091b40c358e9af12b7d62c36345fc25d4515e82ecf84b70840d9eccb1a2462 | Java | 19,699 | 601 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
647d52ff0136631d218a22967b53c3cc6b75f272fbbaa9f7195b0ee1d0ac4c93 | Java | 19,752 | 587 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.ase;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
im... |
f271c9a3a66e0c03ecf0ab435a720675e8e827dc6b44f0ca1ae9c3f002072cfe | Java | 19,904 | 554 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io... |
01858aa1ec35deead808453c5aeff70b0fa9e6b844f5c57169ab7186d6dbea3e | Java | 20,055 | 541 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.util;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.Gen... |
393ea9bcfd06709644ab40a437aa1901973999b693ce9db8aa0f1208a2fe8a59 | Java | 20,230 | 680 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
337bb14ba8bda7f6d7974f9bc0de3679e11ae37daadf257b23b1fa331ce5697a | Java | 20,417 | 523 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.graphics;
import com.itextpdf.text.DocumentException;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Graphics2D;
... |
ae28b64e74cb3c96975bce6bbb2cc7532d5ce4fbb90775b24cd5b1aa9ecab1d8 | Java | 20,505 | 527 | /*-
* #%L
* Mavenized version of the BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code mus... |
5557fdce1800fdf26fe590159118db30606b45856b624ac8d949059aeaab82e4 | Java | 20,557 | 486 | package mbqtl.junk;//package betaqtl.junk;
//
//import betaqtl.*;
//import betaqtl.vcf.VCFTabix;
//import betaqtl.vcf.VCFVariant;
//import umcg.genetica.console.ProgressBar;
//import umcg.genetica.containers.Triple;
//import umcg.genetica.enums.Chromosome;
//import umcg.genetica.features.Feature;
//import umcg.genetica... |
e676e94e7abd0f4d3b2d0e9171b0473a43064c60049c197989f984cd4ab4395f | Java | 20,646 | 567 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import org.apache.commons.math3.distribution.ChiSquaredDistribution;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.EQTL;
import umcg.genetica.io.trityper.QTLTextFile;
import umcg.genetica.io.trityper.util.BaseAnnot... |
064942e78ed2e29859daf8b8ab8d449ae88d947ec665bcbbba21a748c8925ea8 | Java | 21,089 | 562 | package eqtlmappingpipeline.binaryInteraction;
import eqtlmappingpipeline.Main;
import org.apache.commons.cli.*;
import org.molgenis.genotype.Allele;
import umcg.genetica.io.binInteraction.*;
import umcg.genetica.io.binInteraction.gene.BinaryInteractionGene;
import umcg.genetica.io.binInteraction.gene.BinaryInteractio... |
f3493ee75f1f1d0632d1583b52654328229c83d10f79c64c4f73d93bfb800407 | Java | 21,157 | 599 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.matrix;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map.Entry... |
c1ad0cb75ea118da96f194be2833e119bc7b298a7f455adf10b716d1a151e07a | Java | 21,160 | 632 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
9e4e23fd2613421d28e885434898047ddf1b745d705abb80359ec5bba23c6e0e | Java | 21,303 | 715 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
cd0dbe7351e6982c1b6decf16f7455b6e9785861b04500f45e479512277781a5 | Java | 21,450 | 622 | package eqtlmappingpipeline.binaryInteraction;
import au.com.bytecode.opencsv.CSVReader;
import au.com.bytecode.opencsv.CSVWriter;
import eqtlmappingpipeline.Main;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java... |
90d52946ccbb5317c6092dbc3a1d2792ffbba2f824bfe877fb12d15dda049a7e | Java | 21,486 | 701 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
0e194d77f0cb80f3c07d83557cb09f16671b07c51fa50a72960792443171222f | Java | 21,487 | 655 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
e82c0a6937fea78ad0f0fe43271dedee50bdccd96e917a08d3caee7ae32898d2 | Java | 21,531 | 576 | /*-
* #%L
* Mavenized version of the BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code mus... |
e385a6b802841ee5cf3376c0d19a779d3808e8f0de6ef8918d4be26cc3d3a4a2 | Java | 21,724 | 536 | package mbqtl.gfx;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import umcg.genetica.graphics.panels.Panel;
import umcg.genetica.graphics.themes.DefaultTheme;
import umcg.genetica.graphics.themes.Theme;
import umcg.genetica.math.stats.Regression;
import umcg.genetica.util.Primiti... |
acb6c888f840d493a81c55baeb89a57494883f9cb4d4edd22599b8e6887a5034 | Java | 21,736 | 626 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.graphics;
import com.itextpdf.text.DocumentException;
import com.itextpdf.text.Rectangle;
import com.itextpdf.text.pdf.PdfContentByte;
import java.awt.Color;
import java.awt.Font;
import java.awt.F... |
5d23be1551cea4520bd8b282483d00ad4b6f61487202ba93301309377f6c759f | Java | 21,934 | 460 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import ... |
586dba86f621ed5042756435b985e07fd8ba6ec0f71f3d1228859d8c697477ca | Java | 21,944 | 444 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.bgen;
import org.apache.commons.io.FilenameUtils;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypeDataException;
import org.m... |
2ff753d4cead1620e5ce74b1925654791c6c751d87871e3352e5525126016ad1 | Java | 21,960 | 448 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.cellTypeSpecificAlleleSpecificExpression;
import java.nio.file.Files;
import java.nio.file.Paths;
import ja... |
c72cd542e3c3a13112286aab2df82f28a48283c8c18e7708b004044c66b6837c | Java | 21,983 | 664 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
676460b7a1fd59914ef44e4a0744710058ef34a9cbbba6fe6b21536af5e68a47 | Java | 22,123 | 469 | package ebi.spot.neo4j2owl.importer;
import ebi.spot.neo4j2owl.N2OConfig;
import ebi.spot.neo4j2owl.N2OException;
import ebi.spot.neo4j2owl.N2OLog;
import ebi.spot.neo4j2owl.N2OStatic;
import org.apache.commons.lang3.StringUtils;
import org.json.JSONObject;
import org.semanticweb.elk.owlapi.ElkReasonerFactory;
import ... |
a0fad6a93b394ddd1abdeea4f2cf9147a9f738c6cb49715a6e4ccf337c599f6d | Java | 22,225 | 679 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
09913efadd60b15ffc27c9352233db03d3313604a8235f97a6f624e714648bb7 | Java | 22,226 | 524 | package nl.umcg.deelenp.genotypeharmonizer;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.text.DateFormat;
import java.text.NumberFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.HashSet;
import ... |
f891aac42f643ec743b595edd79f32cd6c1435c4ad85122303ebfc4cca3613d6 | Java | 22,241 | 706 | /*-
* #%L
* Mavenized version of the BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code mus... |
5ce9934577a6ff9df46a0a6cc1000cb61a265c9448eaf398872723d771a88fb8 | Java | 22,467 | 708 | /*-
* #%L
* Mavenized version of the BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code mus... |
14d0085cc28244ac3dad1f30c11c1169f948835a00ecb7e37d14e1656b8e373a | Java | 22,655 | 471 | /*)
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.runners;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import java.io.IOException;
import ... |
7929f84298a7381f7ef9c1a5445aff9ac1fc7c230f6b485a9e1a87c6c15fe0c8 | Java | 22,749 | 603 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
7c5b81ffa61b14ebe11b61fea79fff8303a716b8682f1bee726b054b4f6b130b | Java | 22,901 | 575 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import com.google.common.primitives.Doubles;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;... |
2986899a7f338de744a812ade021c4f9efb441bdcf9690e8deb29da2896593e1 | Java | 22,941 | 651 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.mixupmapper;
import eqtlmappingpipeline.metaqtl3.FDR;
import eqtlmappingpipeline.metaqtl3.MetaQTL3;
import eqtlmappingpipeline.metaqtl3.containers.Settings;
import org.apache.commons.configur... |
7eff04a6de9f0ba32f677aeb87ba7cd0b28aba0257fa120cf7df26cda1e95361 | Java | 23,002 | 651 | package edu.cmu.cs.eyetrack.gui;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.GraphicsEnvironment;
import java.awt.GridLayout;
import java.awt.Shape;
import java.awt.Window;
import java.awt.event.KeyEvent;
import java.awt.event.Key... |
d587d4a877d8e7a027e7f50f342f26f778bd5cc5bd600140ffe58610c197b79a | Java | 23,003 | 566 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta.cis;
import com.itextpdf.text.DocumentException;
import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread;
import eqtlmappingpipeline.metaqtl3.FDR;
import eqtl... |
e5662134ecaa490a39bd463298b3fb6e2f8b23e0b49a1a32cd94f7b6624d0250 | Java | 23,084 | 693 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.westrah.binarymetaanalyzer;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.NoSuchElementException;
import java.util.loggi... |
41e567f8c30c7441c2d7caa02a144904f8b216598a2a385ed3426ab2267e320d | Java | 23,112 | 541 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.methylation;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;... |
8aa86dc0b2111918a232809e37197f17b35b58735d4ca2b43c05e123ecea6370 | Java | 23,308 | 1,047 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper;
import umcg.genetica.io.trityper.util.ChrAnnotation;
import java.util.regex.Pattern;
/**
* @author harmjan
*/
public class EQTL implements Comparable<EQTL> {
private Double pval... |
5df90f8c458d358d1f0d5b2d6a5798e510e908bc19874ccfd98e86c2a1c9e785 | Java | 23,629 | 778 | /*
* JCudaUtils - Utilities for JCuda
* http://www.jcuda.org
*
* Copyright (c) 2010 Marco Hutter - http://www.jcuda.org
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* ... |
770ad8c6a463aa19aa1614a2085372fba55fb697992ea5152d64715b3bc83bdc | Java | 23,696 | 516 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Random;
import java.util.Set;
import java.util.concurrent.Cal... |
575db7d0a0644f7f4e71aeca3ca16eb764f0518c847c4e099bdd0750ef8ba298 | Java | 23,741 | 595 | package mbqtl;
import mbqtl.datastructures.Dataset;
import mbqtl.datastructures.GeneAnnotation;
import mbqtl.datastructures.GeneExpressionData;
import mbqtl.datastructures.SNPAnnotation;
import mbqtl.enums.AnalysisType;
import umcg.genetica.containers.Triple;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.... |
14f21a916740f9c2086ad11f760425d018ede609269e3863d591b8175fd28c0f | Java | 23,742 | 771 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
fc31f00287d30b183611d230b0e2da0f5cf47e82996a809c2f58270b9bdc235a | Java | 23,765 | 701 | /*-
* #%L
* Mavenized version of the BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code mus... |
dea9c005460094d79fa33bcffe609f355fbc46f45ece03f8b56d93327de9f66a | Java | 23,767 | 557 | package nl.systemsgenetics.genenetworkbackend.predictions;
import java.io.*;
import java.net.*;
import java.util.*;
import java.awt.image.BufferedImage;
import java.awt.image.*;
import java.awt.*;
import java.awt.geom.*;
import java.lang.Math;
import javax.imageio.*;
/**
*
* @author lude
*/
public class Expression... |
c98f786093230011ea7eee44e35836155a54da3e02097374280d4cce6d8c771b | Java | 23,768 | 643 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.mixupmapper;
import eqtlmappingpipeline.graphics.curve.ROCCurve;
import eqtlmappingpipeline.graphics.histogram.MultiFrequencyDistributionHistogram;
import eqtlmappingpipeline.graphics.map.Mix... |
9b53c2cad6d96a56f3c8c2e7db0cab4c4afdb26ff1680aa8021fc28e902652c3 | Java | 23,868 | 375 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.simplegeneticriskscorecalculator;
import gnu.trove.map.hash.THashMap;
import java.io.File;
import java.io.I... |
9e546aa5dfc14c46317fa8115ac0d7b95855c4d6861e37a7e225d65e0444ee1d | Java | 23,880 | 655 | package nl.systemsgenetics.downstreamer.runners;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.algo.decomposition.DenseDoubleEigenvalueDecomposition;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.C... |
3b06d8abbe527fdfa3954a648f6f03c24adf1e5025b89da69337aac1e2f096a1 | Java | 24,152 | 803 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper;
import gnu.trove.map.hash.THashMap;
import gnu.trove.map.hash.TObjectIntHashMap;
import gnu.trove.set.hash.THashSet;
import org.apache.commons.collections.primitives.ArrayIntList;
impo... |
bac59fd2ea040e8c7f68b4845ecfad1b58d0f397f210be0545bf9850833f509d | Java | 24,159 | 839 | //******************************************************************************
//
// File: NonNegativeLeastSquares.java
// Package: edu.rit.numeric
// Unit: Class edu.rit.numeric.NonNegativeLeastSquares
//
// This Java source file is copyright (C) 2005 by Alan Kaminsky. All rights
// reserved. For further infor... |
90ec285629a519cb23d752f86fddf6641d3b045da15a2ca3fd61b5e73e569e1a | Java | 24,168 | 596 | package main.java.decon_eQTL;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
/*
* Collection of all the interaction models and their shared data (genotypes, expression etc)
* There are n + 1 interaction models, where n = the n... |
0e52934bcea8cc4b3779c572133c68083197178c833b60097e789ccc118f472b | Java | 24,307 | 738 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.pcaoptimum;
import eqtlmappingpipeline.metaqtl3.FDR;
import eqtlmappingpipeline.metaqtl3.MetaQTL3;
import eqtlmappingpipeline.metaqtl3.containers.Settings;
import eqtlmappingpipeline.normaliz... |
3f16a8008f82360b0f04033cf0782f6fca65b25d2bc0137ff8f4a5759af04869 | Java | 24,399 | 575 | package nl.systemsgenetics.genenetworkbackend.predictions;
import java.io.*;
import java.net.*;
import java.util.*;
import java.awt.image.BufferedImage;
import java.awt.image.*;
import java.awt.*;
import java.awt.geom.*;
import java.lang.Math;
import javax.imageio.*;
/**
*
* @author lude
*/
public class Expression... |
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