sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9fa0109f48c1d8d8af43b667620830fc71a778fe7c6c010d8313e4146b1a2e86 | Java | 8,457 | 219 | /*-
* #%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... |
1c327ea5ec9b7af27f8f083e250ea798a6349f6ed5dc810c627ea80817d6ecdf | Java | 8,493 | 253 | package umcg.genetica.io.trityper;
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import org.apache.commons.cli.*;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.... |
16f95876af112b14e193ec9876455bd0298a96796cef47554b03253b7d7d64e7 | Java | 8,497 | 298 | /*-
* #%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... |
9d11a13ea2bcd90eafb5ffd6ae80bb6069395a4d7f871c93ba61c97831dfbe44 | Java | 8,561 | 253 | /*-
* #%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... |
d8baedb377633f46dc87b9bb542e2961e0e8e8624fec789fee6eeae0fbf40489 | Java | 8,577 | 250 | package main.java.decon_eQTL;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.apache.commons.csv.CSVFormat;
import org.apache.com... |
461f1346c88b9501e4956b9483c0c1f59c1d4342ec2477726fbbaf74b47a0533 | Java | 8,596 | 245 | /*
* 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.HashSet;
/**
*
* @author MarcJan
*/
public class MergeDoubleMatrices {
/**
* Merge a matrix based on shared c... |
68028197dddbd3b65be1b55490c7bd90875f89e7c45b20459fd7fbd90f65131b | Java | 8,596 | 213 | /*-
* #%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... |
f1e9d3c0558f999f2a06adad99d7a663ba41dbbd838a0da5fa45c60b5f8b4d79 | Java | 8,651 | 265 | /*-
* #%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... |
2dc535d40dc61db83d5cf5ab9810d7d2ab2ba4aaf36974f2220010d1784e5a5b | Java | 8,657 | 241 | /*
* 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.transCorrelationQtl;
import au.com.bytecode.opencsv.CSVReader;
import au.com.bytecode.opencsv.CSVWriter;
i... |
96cad8e4f230d01f00d2bfb229bdc23241b19365c9dc846209ac010eea96bbf7 | Java | 8,716 | 275 | /*-
* #%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... |
2023e837dc2956be6d6a5bc3d251b6c6df2e5ac99617608d35a603b824826ca4 | Java | 8,719 | 235 | /*-
* #%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... |
69222eab84a91a994783bb7846c528b94639862a4148a8283beef11ef008aa31 | Java | 8,722 | 202 | /*
* DetermineLD.java
*
* Created on August 8, 2006, 4:32 PM
*
* To change this template, choose Tools | Template Manager
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.util;
import umcg.genetica.containers.Pair;
import umcg.genetica.io.trityper.SNP;
import umcg.genetica... |
c88e0d14365caf09e6715a33239adf509ec26263c8b1e84edbdc89d234adc416 | Java | 8,724 | 253 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.normalization;
import java.io.IOException;
import umcg.genetica.io.Gpio;
/**
* @author harmjan
*/
public class NormalizationConsoleGUI {
public NormalizationConsoleGUI(String[] args) {
... |
23553c9cf9914e8fc0a4fb56f25af3947f966d621aa8a2734c7aacc307b2fb24 | Java | 8,739 | 265 | /*
* #%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... |
c568bd4bc3bc86c12fbd2756d3198e19411266863a974e4333c6c211b1b5310d | Java | 8,739 | 265 | /*
* #%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... |
e33edca24f24b583a19448638af52288b55f45b02ebcb868e8c8174b039a6ad1 | Java | 8,777 | 214 | package org.molgenis.genotype.bgen;
import org.molgenis.genotype.GenotypeDataException;
/**
*
* @author patri
*/
public class TmpTest {
/**
* Index is the number of last bits used from the first byte
*/
static final int[] LAST_BYTE_MASK = {255, 1, 3, 7, 15, 31, 63, 127, 255};
/**
* Index is the number of... |
244832f5cdc7d887e2a07c7810adc2969838f7a3e4d89f876e693f3fb3671967 | Java | 8,779 | 206 | /*-
* #%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... |
7291fc825f6203590dea35e62de7360cc85669fab718529e4bcd0896a506919f | Java | 8,786 | 243 | /*-
* #%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... |
e14ad50276b510aaab287f6deedeaa7fd2282bfa0cdb2a263c775baa2d8fc778 | Java | 8,789 | 243 | package umcg.genetica.io.trityper.util;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica.io.text.TextFile;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.u... |
1fa4f1cc3789c0fca39458272b0f0606e9611c52e5b2e591ae09da83cd65d69d | Java | 8,805 | 98 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.ase;
import cern.colt.list.tint.IntArrayList;
import java.util.Random;
import static org.testng.Assert.*;
import org.testng.annotations.Test;
/**
*
* @author Patrick Deelen
*/
public clas... |
98dbdab4e1f51adf7fade3d3243748a82b72e389127229f11b87800465765cf5 | Java | 8,806 | 261 | /*-
* #%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... |
ce1d234cd679efb0168f3361bf4a5fd358106fa3c5d84533019d1ad751bd4a11 | Java | 8,830 | 225 | /*-
* #%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... |
8868633742d729260f7688f165bd93173d58617622ea5c770aa1158857d3373f | Java | 8,843 | 181 | package org.molgenis.genotype.vcf.VcfGenotypeField;
import org.molgenis.genotype.GenotypeDataException;
import org.molgenis.vcf.VcfRecord;
import java.util.Arrays;
import java.util.LinkedHashSet;
import java.util.List;
/**
* Class that picks Vcf Genotype Formats and identifiers from a list of Vcf Genotype Formats,
... |
e28f7ef3c297c7eb5f5e3be2982ec1fb16ff5afb509f0b980020c0deda591abd | Java | 8,877 | 246 | /*-
* #%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... |
362fe21d645ced4d9b71455e59f32513b32e22b449821da5fefd2a3a682c06a0 | Java | 8,886 | 235 | /*
* 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.toolbox.picalo;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVRe... |
1404fc5887f0d9e82b6a5a1371814c6621c7bde02a3dd8729008fbd1e750645c | Java | 8,902 | 220 | /*-
* #%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... |
11a753949cd139636a3c7a30088f290e2abb1d74a53b08284c2eb5a351a54828 | Java | 8,906 | 190 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.conditionalanalysis;
import umcg.genetica.console.ConsoleGUIElems;
/**
* @author harmjan
*/
public class ConditionalAnalysisConsoleGUI {
public ConditionalAnalysisConsoleGUI(String[] ... |
7cbd991e4e164110cf5a8ef29b1c62a669b2ec306dde160f8f023263389481be | Java | 8,907 | 222 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.plink;
import java.io.BufferedOutputStream;
import java.io.BufferedWriter;
import java.io.DataOutputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOut... |
3a383ed3e56aa26fdce2430f415cdc7c5f4480a7df9f007cba736a61ce68c449 | Java | 8,953 | 221 | /*-
* #%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... |
3f09dbcb573575e7f6a1798b460a5416c5df225164774ddef96ee6cb1d1b1b6b | Java | 9,020 | 320 | package umcg.genetica.graphics.panels;
import umcg.genetica.containers.Pair;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.enums.Strand;
import umcg.genetica.features.*;
import umcg.genetica.graphics.DefaultGraphics;
import java.awt.*;
import java.util.*;
/**
* Created by hwestra on 7/17/15.
*/
publ... |
7317b27c5b1f6f420e8757bc10b036fc5d2cccafa214f37b03be1b9f09689535 | Java | 9,065 | 267 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.interactionanalysis;
import umcg.genetica.console.ConsoleGUIElems;
import java.io.IOException;
/**
* @author harm-jan
*/
public class InteractionAnalysisConsoleGUI {
enum... |
8420d39cc48376d756337cb11547e769af1f7393a75ab8178f3a41c9dd6e7e04 | Java | 9,065 | 244 | /*-
* #%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... |
4ded24920608a41e3a86584ce9a84618feb64af57c620cb3b108a7c1c63e582b | Java | 9,083 | 248 | 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.List;
import java.util... |
17b228fc5aea292c54774ad59d45693bda6729daedc0e2ea36ceff5ab459b5f9 | Java | 9,085 | 280 | /*-
* #%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... |
afe607bf3ff0c0836761795249eac0b225a48dc914da4ef778d9184c433cba57 | Java | 9,085 | 259 | /*
* 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.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.io... |
98edfbbf5ee0d9eb9760bc0a0a8e45553c719d7a02ed607e51231ea34c92b319 | Java | 9,111 | 290 | package org.molgenis.genotype.variant;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypeDataException;
import org.molgenis.genotype.util.ChromosomeComparator;
import org.molgenis.genotype.util.Ld;
import org.molgenis.genotype.util.LdCalculator;
import org.... |
4abb707cb271a128a253a8b7519f5512abdc755bab7157dfdd668e4cacead8af | Java | 9,127 | 233 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.graphics;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage... |
0409d37564a8a34136bf3d841c60a4c8879b899844ad36d101ac89d8c3138834 | Java | 9,132 | 214 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3;
import umcg.genetica.console.ConsoleGUIElems;
/**
*
* @author harmjan
*/
public class MetaQTL3ConsoleGUI {
public MetaQTL3ConsoleGUI(String[] args) {
String settin... |
b0cb45057c92b83626a3ef3a3f8c27d1898c32f244f7ca69e2635c1578d6dc7c | Java | 9,153 | 296 | /*
* 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.toolbox;
import htsjdk.tribble.SimpleFeature;
import java.io.File;
import org.apache.commons.cli.CommandLin... |
90d4c041ff7cb78096e46132fe78759155e1f54239d9523f320441a038e2fe92 | Java | 9,160 | 292 | package umcg.genetica.graphics.panels;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import umcg.genetica.graphics.themes.DefaultTheme;
import umcg.genetica.graphics.themes.Theme;
import java.awt.*;
import java.text.DecimalFormat;
/**
* Created by hwestra on 7/16/15.
*/
public... |
2063569a8f7f92a7a2d535cc5ef616753d20bd7ce0854cc0812c2e03db739590 | Java | 9,169 | 191 | package org.molgenis.genotype.bgen;
import org.molgenis.genotype.GenotypeData;
import org.molgenis.genotype.ResourceTest;
import org.molgenis.genotype.RandomAccessGenotypeDataReaderFormats;
import org.molgenis.genotype.annotation.SampleAnnotation;
import org.molgenis.genotype.plink.BedBimFamGenotypeData;
import org.mo... |
e6a5c1381bd643c8ac0a79ccdc65262b571fb1ae466e4a3b3e515c8a25f36386 | Java | 9,170 | 248 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import eqtlmappingpipeline.metaqtl3.EQTLRegression;
import eqtlmappingpipeline.metaqtl3.MetaQTL3;
import eqtlmappingpipeline.metaqtl3.containers.Settings;
import org.apache.commons.conf... |
18ff5a66f5b5bf9d09ca18256fd5ccebfd409df931d10f4e2c0c6205e6064cb3 | Java | 9,184 | 229 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3.graphics;
import com.itextpdf.text.DocumentException;
import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
import j... |
abe82bfd764efe6a2df84493d7df804b42fddd6fcbd7676b45170d1cfef7cc06 | Java | 9,202 | 253 | /*-
* #%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... |
824b2a17265a4a211cfb8ea0524030d6f2e5fdc09a0e53da79941ca6da31dc5a | Java | 9,227 | 268 | /*-
* #%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... |
70a5fcbf19dcf4fc0588da1ecfa784ff727669afb2890293509c8995b950ff88 | Java | 9,240 | 44 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3;
import org.testng.annotations.Test;
/**
*
* @author Patrick Deelen
*/
public class CalculationThreadTest {
public CalculationThreadTest() {
}
/**
* Test of test method, ... |
f7b758b543a1eafa7987505ffd40654e70cdade704a2acf6fc6d0f06f88f9213 | Java | 9,250 | 257 | /*-
* #%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 ... |
e6858939962650834dfa35fafe8f77976ac0cd3c4f90adc21b2689de41a1ba61 | Java | 9,270 | 184 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatrix1D;
import com.opencsv.CSVWriter;
impor... |
4b230c1cf54541d2cedf46e3412354f5813cb9529cf749a3324c5f19dad2c1bf | Java | 9,275 | 242 | /*-
* #%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... |
5dc322d9dee60a25e6287291a73ccac07095cd6c2fa6ad2968e1aad98601f0a8 | Java | 9,279 | 265 | /*-
* #%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... |
128c218079038102065fef73d0d20a31512ff58839d712ab3c714eb64dd8ad35 | Java | 9,307 | 243 | 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.Map;
import java.util.... |
ad333d9679986a6891e0383408d902cb4ddec7c4f51652ae2f1883c8de9bc57c | Java | 9,315 | 333 | /*-
* #%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... |
cd42e11c6f2e318dcaf767ba5d319c9432c1216fdfd41280361755c07d7ba832 | Java | 9,316 | 348 | package network_code_v5.func;
import java.io.*;
import java.util.*;
public class PutativeRegulatoryRegions
{
public PutativeRegulatoryRegions(){}
/*
*
*/
public void genPutativeRegulatoryRegionsFasta(String path, String bedFile, String geneInfoPath, String geneInfo, String geneExpr, String outputPath, St... |
c79e76b0c927de7406e60cfa090c8ba9574c612b17fc2ec058f66526cbb27a21 | Java | 9,325 | 259 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.uti... |
b1fb9bab3bc767d6143dd0fa69678ff15bce2404d3c0f4eb6e020657a0f8e4f0 | Java | 9,353 | 326 | /*
* 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;
/**
*
* @author adriaan
*/
publi... |
a552963a74a87a3be9226a15cb72e9ef338902305e97b57b6a24adff09e59102 | Java | 9,365 | 263 | package org.molgenis.genotype.variant;
import java.util.*;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypeDataException;
import org.molgenis.genotype.util.FixedSizeIterable;
import org.molgenis.genotype.util.MafCalculator;
import org.molgenis.genotype.u... |
48378bef11445179e87cff088244c828518b1350f41730497620a2e8fdebeb18 | Java | 9,371 | 292 | package edu.cmu.cs.eyetrack.gui;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.util.ArrayList;
im... |
36cdee4ec94b0de62fcfaed2de299a2b5cb324f3b42cf9931c32f092fe051684 | Java | 9,390 | 253 | package nl.systemsgenetics.geneticriskscorecalculator;
import gnu.trove.map.hash.TObjectDoubleHashMap;
import java.io.File;
import java.io.IOException;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.regex.Patter... |
a78eeabb4c36cd8c191b57ba75f4761911148414a68e665c09f33bbc146af68a | Java | 9,406 | 287 | /*
* 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... |
2e448c572b59e973a64b719a5336e48b032a12bd9cd4bfba0e308d66b5b2dcca | Java | 9,407 | 202 | /*
* 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.eqtlannotation;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.ut... |
0ad480196e531747b5f7468042f2020ce28b498529f348fdfefc8ae14115ddb4 | Java | 9,440 | 247 | /*-
* #%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 ... |
456ce765412fe93b8b667bddaddc6c978d41be2dc8e16bc6fc583d7726127b6c | Java | 9,461 | 216 | /*
* 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.DoubleMatrix2D;
import cern.colt.matrix.tdouble.algo.... |
b989d2e616ac933f237c69a9fbe11f7b9ff0e34cfb697bd301a09843a4398d71 | Java | 9,468 | 236 | package eqtlmappingpipeline.util;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.util.BaseAnnot;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.ArrayList;
public class GetMAFFromSNPQCLog {
public static void main(String[] args) {
String file = "D... |
566aa9f8771b7977a129d364c7c159de6eee73ef1b284e3e44a74c8cf4c59e6c | Java | 9,534 | 268 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import umcg.genetica.io.text.TextFile;
import java.io.IOException;
import java.util.ArrayList;
public class SettingsFileCreator {
public static void main(String[] args) {
String directoryfile = "C:\\Data\\tmp\\2017-12-27-Standar... |
d1dd03e8815727189a251318fe42a442cbf1bbc1885a8ca7aa92d76ed111277b | Java | 9,552 | 288 | package umcg.genetica.io.fasta;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.Collections;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
... |
a099e618d3c6415a576167a4d6534711fc5cab6d59efb841d623e982ecf7ba2b | Java | 9,568 | 264 | package nl.systemsgenetics.genenetworkbackend;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
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.... |
e30a7eb878142879148914b313b96ecb4fda61ff26ede86b139d9a2d4565b4af | Java | 9,581 | 292 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import nl.umcg.westrah.binarymetaanalyzer.BinaryMetaAnalysis;
import nl.umcg.westrah.binarymetaanalyzer.BinaryMetaAnalysisDataset;
import nl.umcg.westrah.binarymetaanalyzer.BinaryMetaAnalysisSettings;
import nl.umcg.westrah.binarymetaanalyz... |
24fbef7617e75f7e8f4feaaad46bfd97b590670ec09ad08b6f1a2d6f5d3e0884 | Java | 9,591 | 284 | /*-
* #%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... |
9d50d2510ce1ce67be6593c612c44d6e37f26661521aad92811eed2f888d6c0a | Java | 9,600 | 227 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.util;
import eqtlmappingpipeline.binarymeta.meta.MetaAnalyze;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java... |
ed07838b0bcc317202909e9d804ce13b3c5ce72a8e4ae9f623d552c89ff75c96 | Java | 9,620 | 248 | /*-
* #%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... |
98298f6edf77950692a6ef545583ed38258617d138a1cc1f90c75471f44c933c | Java | 9,636 | 272 | package nl.systemsgenetics.datg;
import org.apache.commons.cli.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.io.File;
public class Options {
private static final Logger LOGGER = LogManager.getLogger(Options.class);
protected static final org.apache.common... |
71e8fc8c0192361351e6be052640efba606fbc036fb1834e8457bca8b53ad2f1 | Java | 9,645 | 217 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util.HiC;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map.E... |
38bfdf5d565233430572469a6dce1a45378b1a81eca0a546493858c0e985adfc | Java | 9,652 | 237 | package nl.systemsgenetics.genenetworkpathwayenrichment;
import org.apache.commons.cli.*;
import umcg.genetica.io.Gpio;
import java.io.IOException;
public class Main {
private static final Options OPTIONS;
public static void main(String[] args) {
System.out.println("Gene set enrichment using GeneNe... |
811760041594e42e10d8835a2b4b5bb0e1e31a82c3489a6c111a8b5030521e22 | Java | 9,678 | 303 | /*-
* #%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... |
6a85c22b7699ad95853286666c60bcec7e8675c4c0a7d27862931d77860514d6 | Java | 9,688 | 276 | 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.EnumMap;
import java.util.HashMap;
import java.util.HashSet;
import java.u... |
48f2c8ee6479665b7f7680287cf988938fede8a28929ad19b4969a82dae8bec1 | Java | 9,692 | 257 | /*-
* #%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 ... |
3cc882b43dcdfa47bc772677a51d10691806ff07f96848e0b5ca89c6c43c0207 | Java | 9,755 | 287 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.L... |
a70dfd7a1d5ba465cbb231643a2072f73ef7890a5304b329035fb8c4d15bfc77 | Java | 9,781 | 288 | package nl.systemsgenetics.downstreamer.runners;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVReader;
import com.opencsv.CSVReaderBuilder;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileIn... |
8d09ef551e5e6def534f5e2b1a00b59f9b83b2c3899db1c62a964a7b98d3e23a | Java | 9,787 | 309 | /*-
* #%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... |
df800c62bf03948fe33b953ed7b3ff1ed100ae205937dc3e192ce727a5d1dad7 | Java | 9,791 | 309 | /*
* WilcoxonMannWhitney.java
*
* Created on February 21, 2007, 3:45 PM
*
* To change this template, choose Tools | Template Manager
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
/**
*
* @author ludefranke
*/
public class WilcoxonMannWhitney {
private double k, n, kn, ... |
1375ae7d8994568242e486af5b51383e566c5fec0ef07fb6594eab791896befb | Java | 9,800 | 332 | /*-
* #%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... |
cd24fe75c237bb49941099c8221e419abf3023861ef16c92c64360cb3ec5e20a | Java | 9,819 | 236 | /*-
* #%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... |
0dd3ddd4cc04d31cf651b98f6a11f94444bdb547e49dc10e780d326f73e9c732 | Java | 9,851 | 219 | package eqtlmappingpipeline.util;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseLargeDoubleMatrix2D;
import eqtlmappingpipeline.metaqtl3.FDR;
import eqtlmappingpipeline.metaqtl3.graphics.QQPlot;
import gnu.trove.set.h... |
9c509e8cb2844550015227f5c9991fbc3e3ca6d706c76180088b0d8b25f0872a | Java | 9,857 | 282 | /*-
* #%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... |
7af2d7c97db4510ac5fb2eabb5751436d31271f52513860a4f046a57950f0400 | Java | 9,877 | 259 | /*-
* #%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... |
b5e8c38ed32ccc3699d26086a5bfc1dd7fc1d78effbaa03d918c6e7447ae6375 | Java | 9,917 | 275 | /*-
* #%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... |
d4a5447e97e0adfd2edcb9e8293df84f90b540377279fc046cd0bf36fe00cd4c | Java | 9,972 | 225 | package edu.cmu.cs.eyetrack.helper;
/*
* Copyright (c) 1995, 2008, Oracle and/or its affiliates. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* - Redistributions of source ... |
a7ff36fedbf4cb8fdc07f9e4d34aa0ebe85ef81182106de82d03edd58834daff | Java | 9,982 | 239 | /*
* 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;
import java.io.File;
import java.net.URISyntaxException;
import java.text.DateFormat;
import ... |
65594632835ce347b71d57a8a7be76fc42a895f25239a03521f056c4e862a62d | Java | 9,991 | 491 | package FindPeaks.accessory.classes;
import java.awt.Polygon;
import java.awt.geom.GeneralPath;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Vector;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.gui.ProfilePlot;
import ij.gui.Roi;
import ij.gui.ShapeRoi;
import ij.measure... |
791f5371fa939fd2a8a6a65b7e4b0e6c139f83327a2d63bcd0256a3e5d8eea9a | Java | 10,006 | 263 | package org.molgenis.genotype.util;
import java.util.LinkedHashMap;
import org.molgenis.genotype.variant.GeneticVariant;
public class LdCalculator
{
/**
* LD calculator. Based on implementation of Harm-Jan Westra and Lude
* Franke.
*
*
* @param variant1
* bi-allelic genetic variant
* @pa... |
5eb1b150de5bcca801f3205469a3e0dd0bf2a5b4d4aca02d7112fcec86407377 | Java | 10,008 | 280 | package main.java.decon_eQTL;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.stat.regression.OLSMultipleLinearRegression;
/*
* InteractionModel contains the information (observed val... |
b7452bbf8d17adf3e9d54ad88217c8879a96d23e2f992ef77a197d113e997580 | Java | 10,010 | 273 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.SNP;
import umcg.genetica.io.trityper.SNPLoader;
import umcg.genetica.io.trityper.TriTyperGenotypeData;
import um... |
595d9639309b16c28b0757c74eabdd51e35f115b0a0dac0e2789f420faaa3c7a | Java | 10,096 | 244 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.matrix2;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseLargeDoubleMatrix2D;
impor... |
a5d807818c980ac5c4c764bde778c347148aa7329ca2d06b8f34ed991367c1c8 | Java | 10,117 | 214 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.gui;
import eqtlmappingpipeline.Main;
import eqtlmappingpipeline.ase.AnnotateAseWithSnpEffVcf;
import eqtlmappingpipeline.ase.Ase;
import eqtlmappingpipeline.ase.AseRecalculate;
import eqtlma... |
8ca59127af7f8050ee4e80ee99bd3bf78874803f62bafdbcd112ad1469db3e9c | Java | 10,124 | 374 | package edu.cmu.cs.eyetrack.state;
import java.awt.Dimension;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import org.joda.time.Period;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus.StimulusCla... |
d8ee6e70e0daf2bf3be038d47173d47c5cb3a189712756b36e98541831e24a92 | Java | 10,124 | 310 | /*-
* #%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... |
91cc6007783508e8dae04cf2a3cf8f4e4f9ed462b6ef0e6e420691c046400e25 | Java | 10,159 | 331 | package org.molgenis.genotype.multipart;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.List;
imp... |
d46575ce2a5951884867a1c8ad740c309b523cb815416b27f347b9773c2a5385 | Java | 10,162 | 268 | package eqtlmappingpipeline.ase;
import gnu.trove.map.TObjectIntMap;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
impo... |
f2061d1f788f5a8e5329d36316c16e6ae4d1ffbf5986138cb9a6f3833d9f4c2e | Java | 10,193 | 301 | /*-
* #%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... |
c664688d1f72758a05304feae3a801f5d7522d4f293a18f686d5f5b83b58da70 | Java | 10,222 | 266 | package nl.systemsgenetics.genenetworkpathwayenrichment;
import umcg.genetica.containers.Pair;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.util.Primitives;
import java.io.IOException;
import java.util.*;
public class Utils {
public static HashSet<String> readSet(String limitGenes) throws IOExcep... |
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