sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f70ef7091b20bc84364a106f3b44b11d0df7c7f7b0289164478dc52a2ae111e6 | Java | 4,073 | 121 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.converters;
import java.io.IOException;
import java.util.HashSet;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.SNP;
import umcg.... |
bd1085040dc85e3a2e8a8c84bc82ad671181f7a8783e70b023820bcfe6767336 | Java | 4,087 | 133 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats.concurrent;
import cern.colt.function.tdouble.DoubleProcedure;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdo... |
e439d0da35dae36c670b244e44a8062d6eba614b371099a472416b62be68063a | Java | 4,090 | 118 | /*-
* #%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... |
2c403faa9e3b5fda6806b309b4c146f4326c24cd59be5d84a7f95a786619a188 | Java | 4,091 | 129 | /*
* 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.development.sophie;
/**
*
* @author Sophie Mulc
*
*/
import com.opencsv.CSVParser;
import ... |
f62fda039dc7f365a515977fa303f24759e65876745dde03ff7d10d73d4fc518 | Java | 4,095 | 104 | /*-
* #%L
* Utility classes for 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 must ret... |
dfd9946940866d5aeb171c0579aad42fdb77cde1ca8d88cc022c4677c039361c | Java | 4,097 | 102 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* 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 ... |
38d0796e9b137ef9530882e88cd6cbb489f15808c72cae74e1cad223c02456d2 | Java | 4,105 | 111 | /*
* #%L
* Utility classes for 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 must reta... |
cb0c2e2f25adcd7aa5a5d7cb70757316801c43fbca4b927672ac172354d9fc95 | Java | 4,105 | 111 | /*
* #%L
* Utility classes for 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 must reta... |
b1824d4284e31ec14a4c777bdd7b10e7975258b8452f41ef81c269350d81b355 | Java | 4,107 | 117 | /*-
* #%L
* Ops created 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 abov... |
fee6ca18e99da510a03e4296514528b2aa5104be49b47f1fe6dc00195594aab4 | Java | 4,122 | 101 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* 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 ... |
f361a28f58884a3c0512f727930fa372e5bc9dd0f5d75ccf418f27040aa10a7f | Java | 4,130 | 125 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.oxford;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.nio.charset.Charset;
... |
fe9fff5211356661ab12c8e23d002ef54ec93fa040e51a20492e460f2e264a94 | Java | 4,131 | 133 | //
// Source code recreated from a .class file by IntelliJ IDEA
// (powered by FernFlower decompiler)
//
package mbqtl.datastructures;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Set;
import mbqtl.Util;
import umcg.genetica.io.text.TextFi... |
a94bcecb77ae5dacc2d478b57c3d928eee8538fe2aa07aa376b4788b8f13a578 | Java | 4,157 | 125 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.textmeta;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.concurrent.Callable;
import umcg.genetica.containers.Pair;
import umcg.genetica.io.trityper.EQTL;
import umcg... |
e0b56361db206ef0462f1603e1fd9fe4df6b69fb61d067f56827a65ff0aa28d3 | Java | 4,168 | 101 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* 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 ... |
50a8b99a16f69fa4b99edb727a20931df1eb198238f8ff0cbe1d4ab5e35a8ab6 | Java | 4,169 | 137 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.regulomedb;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;
/**
*
* @author Pa... |
6cb4fd7be9591f7aa148bd7799f32fa37b6a3954086604ca280c72fed7dc9073 | Java | 4,175 | 151 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import java.io.IOException;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.molgenis.genotype.AbstractRandomAccessGenotypeData;
import org.... |
00721d2662c2ff205ef59ce6bc9635b18984cf3a1e5d201a316ee10a4cc1e5a2 | Java | 4,181 | 133 | /*
* 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 org.apache.commons.math3.distribution.BinomialDistribution... |
7847db6446586be175209222208a84d0ae4cd41a1d33756afdbb1498e8879e12 | Java | 4,190 | 114 | package eqtlmappingpipeline.util;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.math.stats.ZScores;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.HashMap;
public class ReplaceBeta {
// WARNING: this code assumes that N is equal for each eQTL (which may not be the ... |
c347de23941d217c9d1e337ac82da64ba9dec26b8b9ebe3c0b62840ece850d04 | Java | 4,193 | 101 | /*
* Copyright (C) 2016 adriaan
*
* 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.
*
* This program is distribute... |
ba7e01142c9d047156cff837658a72c46b3613d262fc1c983fdcc500fbaf75b6 | Java | 4,204 | 154 | package umcg.genetica.features;
import umcg.genetica.containers.Pair;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
/**
* Created by hwestra on 5/13/15.
*/
public class FeatureMerger {
public static ArrayList<Feature> merge(ArrayList<Feature> f, boolean returnCopies) {
// ... |
37158d67bb75e6ea3cc688a5d3b789c88d381345e721b8b9959c4a1d18a9302e | Java | 4,219 | 127 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.concurrent.LinkedBlockingQueue;
import umcg.genetica.console.ProgressBar;
im... |
578ecc8ddb07d7e77e25af0c2099582cfffc360c4def4a111b35c0e3de0865ce | Java | 4,219 | 102 | package org.molgenis.genotype.vcf;
import static org.testng.Assert.assertEquals;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.molgenis.genotype.Allele;
import org.molgenis.vcf.VcfRecord;
import org.molgenis.vcf.VcfSample;
import org.molgenis.vcf.meta.VcfM... |
f9c6fbf65a4ab36b3ed618b3bbb1c53fc791227d478c5a49b99e6903af9c8ed7 | Java | 4,234 | 160 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.westrah.binarymetaanalyzer;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuration.XMLCon... |
dfe821b37affb2d111cedcc9a4aff97964583ff89924d3cc93210c22f3227662 | Java | 4,242 | 151 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import java.io.IOException;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.molgenis.genotype.AbstractRandomAccessGenotypeData;
import org.... |
56bf0e8cb84bcd4a2ebcb2ff0b293651a310ef8b7cad85bdaacd9ef447703a31 | Java | 4,248 | 80 | package ebi.spot.neo4j2owl;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.*;
public class N2OStatic {
private static OWLDataFactory df = OWLManager.getOWLDataFactory();
public static final String OBONS = "http://purl.obolibrary.org/obo/";
private static final Str... |
8567c7f203a2b52c1886f1d0e12a291d02596503b1b3897fcb1167780f8fea7c | Java | 4,251 | 128 | /*-
* #%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... |
eb52b3c236484f2b75ddc7a91db0933a0d23f62a5a05b9a51e36ea677011b894 | Java | 4,258 | 166 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import java.util.HashSet;
import org.molgenis.genotype.RandomAccessGenotypeData;
import org.molgenis.genotype.RandomAccessGenotypeDataReaderFormats;
import org.molgenis.genot... |
005ca11f2f969626a3999bf9ef3038caf212eb1e72f8e03a8e00eb354cdcb27e | Java | 4,263 | 131 | /*-
* #%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... |
903ae3b8e93e4b4ab76fba459314e5d39e4f47f76bf4285c515058cb63752a86 | Java | 4,263 | 113 | package edu.cmu.cs.eyetrack.analysis.score;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import edu.cmu.cs.eyetrack.analysis.score.compare.PointComparator;
import edu.cmu.cs.eyetrack.analysis.score.distance.DistanceFunction;
import edu.cmu.cs.eyetrack.ana... |
01eb868f849327396cb374ba7fcf7051726b1377a02a6a7209946df788a54c74 | Java | 4,290 | 131 | /*
* 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.genenetworkbackend.div;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.openc... |
2c1b25bdae4401fab4f39d47ff41cc2691ca2094717bfb2bffd63ddfd569b1cc | Java | 4,294 | 99 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import umcg.genetica.legacy.ExpressionDataset;
import java.util.HashMap;
public class NullSetGenerator {
public void generateTPAndTNSet() {
// //Directory holding the Z-Score matrices:
// int nrPermutedZScoreMatrices = 10;
// Stri... |
2c5b488b3550ec706224789425f9268bbde42de98224f61d1e62a4cba9b4da21 | Java | 4,296 | 128 | /*-
* #%L
* Utility classes for 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 must ret... |
e37644e0b1e1e584d674503ab3461685704a0d2626464b30c72b76b37a38b93e | Java | 4,311 | 131 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.ucsc;
import java.io.IOException;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.util.ChrAnnotation;
import umcg.genetica.text.Strings;
/*... |
a8d9de5673438d9208b5e420f4e7d28218f853b2518bef4d1b07fb92299c2da2 | Java | 4,323 | 149 | package umcg.genetica.io.plink;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import umcg.genetica.enums.DiseaseStatus;
import umcg.genetica.enums.Gender;
import umcg.genetica.individuals.Family;
import umcg.genetica.individuals.Individual;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hash... |
3c91c14dd91fa5448b1d475b80ba94209ca722f9a1dd9dcdd1a33fd77813e515 | Java | 4,350 | 148 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.westrah.binarymetaanalyzer;
import org.molgenis.genotype.util.ChromosomeComparator;
/**
*
* @author harmjan
*/
public class MetaQTL4MetaTrait implements Comparable<Object> {
static boolean mapsT... |
e1e415a6b14af599d73083860a8e77d4b471271d2a08f3e6bb496d003b0e480d | Java | 4,357 | 138 | package nl.systemsgenetics.downstreamer.summarystatistic;
import cern.colt.function.tdouble.DoubleDoubleFunction;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import org.apache.commons.lang3.NotImplementedException;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import java.util.Collection;
import nl.syste... |
58f707adc2e4c19dcf0c77b0f5b2b0c57ec88f8ac56df8808036b09cfc25d77f | Java | 4,360 | 136 | /*
* 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.functionenrichmentoftransqtls;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.jet.random.tdoub... |
c2a1a191c811290fb197e37ab2827b5fb2af4e6c68a2dc0dbc4f23739fa23f10 | Java | 4,362 | 128 | /*-
* #%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... |
469b806c3f1a14940f11e665c19ea472567256a555aebfa13dfe17d202bac76b | Java | 4,365 | 243 | package umcg.genetica.features;
import umcg.genetica.enums.Chromosome;
import java.util.Arrays;
/**
* Created by hwestra on 11/11/15.
*/
public class SNPFeature extends Feature {
double p;
private double imputationQualScore;
private String[] alleles;
private String minorAllele;
private double maf;
private... |
cf6ab052887d7250c9dd5755fd0c84aa1b73745bc3a3175ae8d3d97522a3a547 | Java | 4,373 | 134 | /*-
* #%L
* Utility classes for 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 must ret... |
a1c42bdc7f70e7fd5342aa8d04451161530cb8e41da0826db77c34474c52990e | Java | 4,376 | 194 | package eqtlmappingpipeline.ase;
import cern.colt.list.tdouble.DoubleArrayList;
import cern.colt.list.tint.IntArrayList;
import java.util.ArrayList;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.variant.id.GeneticVariantId;
/**
*
* @author Patrick Deelen
*/
public class AseVariantBean implement... |
a870d6146c151637b9850d6cfe55d70536dede192ccdd807890d25840dfa1e33 | Java | 4,384 | 112 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline;
import eqtlmappingpipeline.util.QTLFileSorter;
import java.io.File;
import java.net.URISyntaxException;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date... |
78efda1ba18262e89c5da0cf8f684ad3520df88fcb4576f00fc695c04229091c | Java | 4,387 | 110 | /*-
* #%L
* Ops created 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 abov... |
19b31283a520e0bbf26296c3bb0090d8db432bf87214158ad63a1b4060b8407d | Java | 4,389 | 147 | /*-
* #%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... |
d4cfd837b0f7209f909a1632c72888ac45009f3d9f263baeeac3ad7e20215107 | Java | 4,389 | 110 | /*-
* #%L
* Ops created for BoneJ2
* %%
* 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 abov... |
ebcb63d78fc90f7137f3784fd32cc01906b1e045efe73e8bf62c345166c1bbaf | Java | 4,389 | 110 | /*-
* #%L
* Ops created 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 abov... |
ca1bdebfe345c56848ff11512b3aea57fbc49b296f76b2a59c21de39e4c0abe3 | Java | 4,391 | 120 | /*-
* #%L
* Ops created 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 abov... |
604c1d55bb2f666855e4f72b69cb15e93d60f7111276c95dd4c697248c9ab427 | Java | 4,396 | 109 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.IOException;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map.Entry;
import java.util.TreeMap;
import java.u... |
4fa01945df41a91069cd4940a32f9ea793852e28230346f4d50b210ebc5400f9 | Java | 4,406 | 116 | /*-
* #%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... |
15733b5351acd21e24463541f01560590a3d5161bfac5e9192e8fffbe9838519 | Java | 4,418 | 131 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta.cis;
import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread;
import java.nio.ByteBuffer;
import java.util.ArrayList;
import java.util.HashMap;
import java.ut... |
96243215d7d33b3be8da7a0125a486526079281109d64ccb766021affea09881 | Java | 4,419 | 118 | /*-
* #%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... |
f9d4c5e4b78658d09eb777467d5c896867fafc57ef4f2ff4207df73a025a6075 | Java | 4,424 | 103 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* 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 ... |
cb0e6e40594c9dc5a65d7b61c788b3d5f8fc33fc4043dfcbd86fb8e1954aada0 | Java | 4,436 | 88 | /*
* 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.options;
/**
*
* @author patri
*/
public enum DownstreamerMode {
// Runners for t... |
d31d40ed6fc618be521bb1f7641df9d75b8a2c9da29fa4d7e8354958dbe7efc8 | Java | 4,436 | 116 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import umcg.genetica.containers.SortableSNP;
import java.util.ArrayList;
import java.util.HashMap;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.util.ChrAnnota... |
cd827a0e4db7429720d3258d3023196a0a006ab77e8c9c480960750a2858d154 | Java | 4,439 | 170 | package umcg.genetica.io.plink;
import umcg.genetica.enums.DiseaseStatus;
import umcg.genetica.enums.Gender;
import umcg.genetica.individuals.Family;
import umcg.genetica.individuals.Individual;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.Arra... |
4378459415f9bc68cd3fba70de98da26c8ff25470a7709e65f4e734d2999081c | Java | 4,440 | 152 | /*-
* #%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... |
778e15009d6f4fceddc556084076950180507b70f2bb4e934b6065641d057e17 | Java | 4,449 | 134 | package eqtlmappingpipeline.ase;
import java.io.BufferedReader;
import java.io.FileReader;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.regex.Pattern;
import org.molgenis.genotype.plink.BedBimFamGenotypeData;
... |
049b56f7748c785bbd906846a2536a9b8ac9ad6950f047a0c9b7b9b64eb43ca5 | Java | 4,457 | 151 | package org.molgenis.genotype.modifiable;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.RandomAccessGenotypeData;
import org.molgenis.genotype.variant.GeneticVariant;
import org.molgenis.genotype.variant.id.GeneticVariantId;
import org.molgenis.genotype.variant... |
158e3a6736ed4b56c5bb75c165565ee749b8f2fc130af6b13520e7b64275073a | Java | 4,457 | 134 | /*
* 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.development.sophie;
/**
*
* @author Sophie Mulc
*
*/
import com.opencsv.CSVParser;
import ... |
e67a4a8d80c908b9b88467375d75995d5e7572857fba27686a7eff40b9e3ebfc | Java | 4,458 | 107 | /*-
* #%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... |
11a940d6ee66111563d3813a62bada0510834d712a3810e85e0fb019d930066d | Java | 4,463 | 143 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.graphics.histogram;
import eqtlmappingpipeline.mixupmapper.stat.dist.Bin;
import eqtlmappingpipeline.mixupmapper.stat.dist.DiscreteDist;
import java.awt.Color;
/**
*
* @author harm-jan
*... |
7c059ea076df240074f36f6432b5ec8fd4d76073110dfe5905f3e0daeb1e24e0 | Java | 4,466 | 112 | /*-
* #%L
* Ops created for BoneJ2
* %%
* 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 abov... |
82553cfe08302e4943df110b9399901f8de5968d63f543346c3c31445b51d736 | Java | 4,471 | 151 | /*
* 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.genenetworkbackend.div;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.openc... |
a39dbde7de1270d103d87532535a4ad4575f82bd9f47d3f247306e40be3413db | Java | 4,474 | 177 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.mixupmapper.stat.dist;
import eqtlmappingpipeline.graphics.histogram.FrequencyDistributionHistogram;
import eqtlmappingpipeline.graphics.histogram.Histogram;
import java.util.ArrayList;
impo... |
0e6f2a84b36d86bc01f5e49d3443cd84c2b83593eca497b4fc080d845617eb3f | Java | 4,495 | 119 | /*-
* #%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... |
299dc4914afcd402dabe3e47024ad01fe83a1c673dbdfa0294b6e7261125340d | Java | 4,499 | 159 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.util;
import com.itextpdf.text.DocumentException;
import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread;
import eqtlmappingpipeline.metaqtl3.FDR;
import eqtlmapp... |
47643ffe979c6bf9724fa824b5398a849165be0202cd0a43e7a49d31151cc1db | Java | 4,513 | 170 | /*
* 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 umcg.genetica.features;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.enums.Strand;
import java.util.ArrayList... |
a3a9f5f5c4fbcf476ab45c5229619ec2ec452f01ece063984b3a7cb4d4c57124 | Java | 4,515 | 146 | package nl.systemsgenetics.genenetworkbackend;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVReader;
import com.opencsv.CSVReaderBuilder;
import java.io.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import ... |
829864800b42394e9711baf51bb3e4a7ea61b47804f28a7d527e90ac562990a3 | Java | 4,516 | 130 | package network_code_v5;
import network_code_v5.proc.*;
import network_code_v5.beans.*;
import java.io.*;
import java.util.*;
import java.lang.*;
/**
* to compile the code: under regulatory_network folder run javac @networkCodeSource.txt
* then run java network_code_v5.NIDataHandler
*
*
****************** for ... |
a7e1a4220ffb11e9e7a1a94872426ef2ea4d49949c055e55288e24dff6239ac9 | Java | 4,520 | 116 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.qcpca;
import umcg.genetica.console.ConsoleGUIElems;
/**
*
* @author harmjan
*/
public class QCPCAConsoleGui {
public QCPCAConsoleGui(String[] args){
String set... |
f2d47edcbd708298e0e49b6b7d955488981b3186b9298166bb14627199088bb4 | Java | 4,527 | 110 | /*-
* #%L
* Utility classes for 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 must ret... |
85b1f41a98ad6b7ba04ed6e3aa6786f99ebf2d6d15d5edabbcfca04257d92022 | Java | 4,533 | 143 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta;
import umcg.genetica.io.trityper.probeannotation.ProbeTranslation;
import eqtlmappingpipeline.binarymeta.meta.graphics.MultiVenn;
import java.io.IOException;
import java.util... |
0371f87b2349dfda104736f0db859b65aa152e8e4e7f5e4f522c33e654973b18 | Java | 4,535 | 117 | /*-
* #%L
* Utility classes for 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 must ret... |
7346c327c99f765e4a38a9c5ac813c60abd6e98cac8bf02f9e762f5742a7a836 | Java | 4,560 | 113 | /*-
* #%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... |
0e608584205a301a718f2599ac705abe2061a28c76734447e82f802b7f3e3ef5 | Java | 4,572 | 152 | package org.molgenis.genotype.plink;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import org.molgenis.gen... |
fdf6565fd696182c3efd5368059612dfd40c3206b789554f032b1dac9e08dd2a | Java | 4,584 | 195 | /*
* 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.util.ArrayList;
import org.jdom.IllegalDataException;... |
15e0a4356dc674ede0b0278ce8fb62eb8ba34852fe801d38267a7e7339968523 | Java | 4,588 | 146 | package nl.systemsgenetics.functionenrichmentoftransqtls;
import cern.colt.function.tdouble.DoubleFunction;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import java.io.IOException;
import java.util.*;
public class ConvertToChiSq {
public void run(String traitfile... |
576267f490be65c1910eadb53599805e4d992a5a792f9b4bb5081260b5aa04d9 | Java | 4,595 | 143 | /*
* 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.gadocommandline;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVR... |
fd4185b9f3d9ef940febe683af154759fcef8bee33fc715be0d1e3ba7b0dd860 | Java | 4,595 | 133 | package nl.systemsgenetics.downstreamer.runners.options;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.molgenis.genotype.GenotypeDataException;
import org.molgenis.genotype.RandomAc... |
c35ea93088ada76daf008b69bffbfd3addcfcad8d27b646b5e995a40ec7720b4 | Java | 4,602 | 117 | package umcg.genetica.math.matrix2;
import java.io.IOException;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.*;
public class Example {
private static void example() throws Exception {
//Creat link to datg file only reading the row names and column names into memory
... |
48fd10695e424bdd7afb7a18552c257dc645b31945f5dab7e389ac11b6f7b31d | Java | 4,605 | 104 | /*-
* #%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... |
8acd143c024481fe54549a196bc76b45e5dc0e7c935090ac2986bb3edbfa4138 | Java | 4,609 | 118 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map.Entry;
import umcg.genetica.io.text.TextFile;
import cern.jet.stat.tdouble.Probabili... |
921443a99cf066af2851a31e02c0c648e9af9f49491d3ac9bc127e6a359a201d | Java | 4,613 | 165 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import umcg.genetica.containers.Pair;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.HashSet;
public class QTLFileFilter {
public static void main(String[] args) {... |
2ea6f1bbbffc1fe1ba16484f4df84fb4fd88986a44863a165b0399695d4b71c1 | Java | 4,640 | 112 | /*-
* #%L
* Ops created 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 abov... |
d903bdc3657a5bf056acd7f9b004141a37ba80765bdc7ac56d393e2a9f525af5 | Java | 4,640 | 112 | /*-
* #%L
* Ops created for BoneJ2
* %%
* 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 abov... |
6ba3492287dbed63145b17bd0d404afdaf021f7150c2f70c00058f6d617213d8 | Java | 4,641 | 132 | /*-
* #%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... |
9095b7d640cf9a65508be9e591719642fd00c05c872ff3749349c89c71f58974 | Java | 4,641 | 140 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.plink;
import java.io.File;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import org.molgenis.genotype.GenotypeData;
import org.molgenis.genotype.Ra... |
32f4aab55b73ee74b8893407e8005cac80354c465cd40a840f7050b51e53c10d | Java | 4,655 | 144 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.containers;
/**
* @author harm-jan taken from :
* http://stackoverflow.com/questions/521171/a-java-collection-of-value-pairs-tuples
*/
public class Pair<L, R> implements Comparable<Pair<L, R>> {... |
36281ddf7b79ab96f9b522f4bf3ce3957d84f7be84a83d440cd6ef31c51c659c | Java | 4,671 | 157 | package eqtlmappingpipeline.util;
import umcg.genetica.containers.Pair;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.EQTL;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.HashMap;
public class ReplaceQTL {
public static void main(String[] args) {
Stri... |
bbaa1210732a64cfe0c42cbdb86cc7a0b167cff28f7d3a7135123e540286a1e6 | Java | 4,679 | 117 | /*-
* #%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... |
ab77e229a03855f5a8dcbde7e5f40fe35ca581d0edad93be6d384289c9efa954 | Java | 4,682 | 151 | package edu.cmu.cs.eyetrack.gui;
import java.awt.CardLayout;
import java.awt.Color;
import java.awt.GraphicsEnvironment;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import javax.swing.JFrame;
import jav... |
4f3dde0e1c3c93b794d5420f02cb51e1749b0788df5b17b488599a719538b76a | Java | 4,687 | 128 | package umcg.genetica.math.stats;
import umcg.genetica.containers.Triple;
import umcg.genetica.util.Primitives;
import java.util.ArrayList;
/**
* @author harmjan
*/
public class Heterogeneity {
public static Triple<Double, Double, Integer> getISq(ArrayList<Double> isqd, ArrayList<Integer> isqn) {
... |
eea35cb29b2bbf82ae18d517236511f51034cbb4305609b89d05d97e222a79f6 | Java | 4,705 | 114 | package main.java.decon_eQTL;
import org.apache.commons.math3.distribution.NormalDistribution;
import JSci.maths.statistics.FDistribution;
import java.lang.Math;
/**
* Several functions for statistical computations
*/
public class Statistics {
/**
* based on https://www.researchgate.net/post/How_do_you_calculat... |
ca3d5c1f704df0cc06803ae65fbb60cf2eeea6177f44b5f9e9a8a475d4e239b4 | Java | 4,712 | 184 | package umcg.genetica.graphics.panels;
import umcg.genetica.features.BedGraphFeature;
import umcg.genetica.features.Feature;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import java.awt.*;
import java.io.File;
import java.util.ArrayList;
/**
* Created by hwestra on 12/3/15.
... |
812d01c4389ab0eb39464340e4cb86489c3cd19332cbf01eabd682fd5f715b69 | Java | 4,716 | 171 | /*-
* #%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... |
621e4a843ec2213372db62faefeef2aba5748edb0faf6814c9d06a0a7067b363 | Java | 4,721 | 144 | /*-
* #%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... |
33785f1e7c945b40d7a3c06a026c05a1eeba60f7152d1a91b281ef3c0bfaf42f | Java | 4,722 | 140 | /*-
* #%L
* Ops created 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 abov... |
29528f28133f2fc59c21e3f47f415af85aef30f71d17f1da70ba7dd1794293d8 | Java | 4,725 | 132 | /*
* 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.io.BufferedReader;
import java.io.File;
import java.i... |
347a19f276c2ef3effcd7210580aa3f4832e88b0a134bf821f8e726b8b8efdb7 | Java | 4,733 | 135 | /*
* 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.gene;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java... |
3ba11f380f3d6f31aeea78847ceaa860304434fa9861d6f561b5b3ec2aa69eb0 | Java | 4,746 | 147 | /*-
* #%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... |
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