sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4461853fef1926f9d53426dcaef2400d2d2cfdfca57ae775f8264471d17067d2 | Java | 24,448 | 469 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import umcg.genetica.io.trityper.probeannotation.ProbeTranslation;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import... |
d994c1db35ded00fe7453e9e3811d67039aff45d1120d309a42d56fd1583ac15 | Java | 24,487 | 717 | /*-
* #%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... |
de83b8dea47f39763d6fce0e273976e75849cefa622214902b30841af1a96259 | Java | 24,564 | 719 | /*-
* #%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... |
5ab86f1f8c8d4c931e7d2db15d0da42ea1ae003980fe54c2ef8487fe39f316ff | Java | 24,663 | 580 | /*
* 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.HashMap;
import java.util.HashSet;
import java.util.regex.Matcher;
import java.... |
82113b63e46e0747229a3d2d378ad245db9a2987bd4042a5b01b4b601f33a0cf | Java | 24,752 | 629 | package umcg.genetica.methylation;
import JSci.maths.ArrayMath;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.... |
7d66d12605bb66cee2b0b8121580b1cf35406962237682efea28e70284ee456e | Java | 24,788 | 583 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
import java.io.*;
import java.net.*;
import java.util.*;
import java.awt.image.BufferedImage;
import java.awt.image.*;
import java.awt.*;
impo... |
f57e83ca57002ce715661aacb755ea3cc3a9a0ff678b4af7bb51c54dac894d36 | Java | 24,955 | 868 | /*-
* #%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... |
c28bc4cd19d19b9bcabb2fd67ece1a198150fd290bb8c795e31cbfb62ad497da | Java | 25,038 | 766 | /*-
* #%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... |
977877485617fdb5fc30915c668b8608f37af9640bbe2bbc4cabd9eceb47aa4c | Java | 25,119 | 723 | /*-
* #%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... |
62de70df30bca3b046ae5ff5f9dfcc138c7c9f0a7cda30bb25e1022df6ce73a5 | Java | 25,323 | 788 | package nl.systemsgenetics.genenetworkpathwayenrichment;
/**
* Created by hwestra on 10/26/15.
* Derived from Scott. A. Czepiel's implementation (http://czep.net/)
*/
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.algo.DenseDoubleAlgebra;
import cern.colt.matrix.tdouble.impl.DenseD... |
aefdcbf6c848dcc478c1302e9d1dc44658a7342735586233aaee94c4ef095f32 | Java | 25,593 | 615 | /*
* 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 htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRec... |
03424cf2fd3738e7dbddbbc74f02d75fcf27acfaf97dd0e946831bb75e1982cc | Java | 25,648 | 653 | /*
* 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.math.matrix2;
import java.io.*;
import java.net.URISyntaxException;
import java.nio.file.FileSystems;
import jav... |
e647a6c5d7322b678210e48ee1f510e002603e2cc6c9a7524e00fb91f590826d | Java | 25,822 | 915 | /*-
* #%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... |
9324361dbddbf1bb790e585fc4c29872581491d955e11926760c1481a6243c09 | Java | 25,879 | 574 | package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
import au.com.bytecode.opencsv.CSVReader;
import au.com.bytecode.opencsv.CSVWriter;
import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.Fil... |
df08b84a00d5857e8b72a4fa8fa2e947dd38e02357b2439229e9e9d7d42ed0c5 | Java | 26,159 | 697 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package imputationtool.postprocessing;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.regex.Pattern;
import umcg.g... |
b8aa076a020c02c3ff9ec5faadbe54b5a04ad222df2c83210ea730b8da8725b9 | Java | 26,224 | 649 | /*-
* #%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... |
1adaa90a0e1fe5a5ba4366b78ce508b577ac13bed4fefdf0f3e802c6a4e63657 | Java | 26,286 | 616 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.development.originalLude;
import java.io.*;
import java.util.*;
/**
*
* @author lude
*/
public class ExpressionDataset {
public double[][] rawData = null;
public int... |
2a6c87d2bf11b079c540d290bf7b1f0de78512c62dcbfa66178675ec1257a261 | Java | 26,633 | 922 | package nl.umcg.westrah.binarymetaanalyzer;
import nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc.*;
import nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc.ld.BinaryFileLD;
import nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc.ld.BinaryFileSorter;
imp... |
99d26ec2723ee033b0d47db994da57305e6a93dba4b715dc4ab611637055e110 | Java | 26,870 | 633 | package eqtlmappingpipeline.binaryInteraction;
import au.com.bytecode.opencsv.CSVWriter;
import eqtlmappingpipeline.Main;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IO... |
5e206e840e4bafb65281d6ab2349e9f2b8b550ea3b43a7a04a9a07984943124f | Java | 26,981 | 656 | /*-
* #%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... |
ecf84168f5ceb5c092d289049c31390b7b89bff4cf408c991bb0006e630ac998 | Java | 27,689 | 600 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.interpolation;
import umcg.genetica.math.Fmath;
import umcg.genetica.util.Primitives;
/**
* ********************************************************
*
* Class CubicSpline
*
* Class for p... |
219f286b13d5db5984f462b476f6e42ce3780edb612ab3e52159e6a786e0e56a | Java | 27,727 | 507 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util.HiC;
import static eqtlmappingpipeline.util.HiC.HiCQTLAnnotatorSnpBased.getNumericResolution;
import static eqtlmappingpipeline.util.HiC.HiCQTLAnnotatorSnpBased.readInQtlInformation;
imp... |
acb4c23b9e5a6e45dd4222a682c448acb136abbebc81d152eae5b4a0511eee25 | Java | 27,855 | 726 | package edu.cmu.cs.eyetrack.analysis.io;
import java.awt.Dimension;
import java.awt.geom.Rectangle2D;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util... |
94935c7423115443d8be0e9119fbb8942cd0af6583982c806f6bae6a31aad8dc | Java | 28,110 | 707 | package nl.systemsgenetics.datg;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import umcg.genetica.math.matrix2.DoubleMatrixDatasetRowCompressedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.nio.file.FileSystems;
import java.tex... |
c64ab6a0b6ace91546cc765fcaa021e30a259b96725396d2614fbf3a9daa048f | Java | 28,194 | 778 | package org.molgenis.genotype.modifiable;
import static org.testng.Assert.assertEquals;
import static org.testng.AssertJUnit.assertNull;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;... |
df0f3245c70a99c52097b011b371d837340a0abbc1e599c7278334ed162d91d6 | Java | 28,336 | 704 | package nl.systemsgenetics.datg;
import com.opencsv.*;
import net.jpountz.lz4.LZ4FrameOutputStream;
import org.apache.commons.cli.ParseException;
import org.apache.commons.collections.CollectionUtils;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import umcg.genetica.math.matrix2.DoubleMatrixDatasetRow;
impor... |
5a15e2b3298db050e9a56316d29f833a36072d7019ad1e394d3fbd6fe7b642b8 | Java | 28,435 | 722 | package eqtlmappingpipeline.ase;
import eqtlmappingpipeline.Main;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
impor... |
9f7a78c506af5e1d7ff5a75ccae65aa7614b4ddedb3c7c9377cb0a446cdf6be7 | Java | 28,450 | 376 | /*
* 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.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.regex.Pattern;
import umcg.genetica.io... |
790c804c59e1630da1681cf4c032f5b9b7b34d0bb6777de558078e555d8c13e0 | Java | 28,540 | 687 | /*
* 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.HashMap;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
i... |
5a24e557bce63c8d46fbb7833b83cb981260e40b9f7a979ab6ed92b3a90e918f | Java | 28,573 | 801 | /*-
* #%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 ... |
258fafe7502dd5c2d3ab63880d62b2d2e67a18cccb1da3ea8e706bf24db70069 | Java | 28,677 | 605 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.bondermj.pcoa;
import cern.colt.matrix.tdouble.algo.DenseDoubleAlgebra;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.imp... |
73fa82b431cb32c4d695b6845911e1882a8163f19254fb99eb751043e02771f0 | Java | 28,790 | 480 | package mbqtl;
import JSci.maths.ArrayMath;
import com.itextpdf.text.DocumentException;
import mbqtl.datastructures.Dataset;
import mbqtl.enums.MetaAnalysisMethod;
import mbqtl.gfx.ForestPlotEQTL;
import mbqtl.gfx.ForestplotPanel;
import mbqtl.gfx.QTLPanel;
import mbqtl.stat.FisherWeightedMetaAnalysis;
import mbqtl.st... |
2e8e90588a5a3b7f837b05c6d4e332a975c7f7ee5f67308a419713dcf2993028 | Java | 28,906 | 603 | package umcg.genetica.methylation;
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.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.logging.Level;
import java.... |
8203185c84748851c76ab0b4f77224ea80dae4a471957ce22e54b30318443051 | Java | 29,157 | 605 | /*
* 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.Graphics2D;
import java.awt.RenderingHints;
import java.awt.Stroke;
import ... |
2e40a72e7c1a93c6374fe978bd59593a2217ab20686ebe8b827a64247fd733a4 | Java | 29,253 | 772 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuratio... |
dbc61896204f0c783312326422a64214c74ea825ac59645aba9fe05e277881f9 | Java | 29,285 | 552 | /*
* 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.Map.Entry;
import java.util.log... |
c6ea59e0fbfe16a2a9243d823e66f5013d74bc398b811f9fcf67f02e37954464 | Java | 29,603 | 912 | /*
* 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.Collections;
import java.util.HashMap;
import java.util.HashSet;
import umcg.genetica.console.Progre... |
414a6cc13e6580dc9df65350802a61bd095881eef315638a1e4cf927f8215f14 | Java | 29,828 | 560 | package mbqtl;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import mbqtl.datastructures.Dataset;
import mbqtl.stat.RankArray;
import mbqtl.vcf.VCFTabix;
import mbqtl.vcf.VCFVariant;
import org.apache.commons.math3.linear.SingularMatrixException;
import org.apache.commons.math3.stat.regression.OLSMultipleLinearRegre... |
4dae9b0e5e5609e134577ad6cac9b02e0ca617c564d48c1086a3f4b515f64603 | Java | 29,898 | 872 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3;
import cern.colt.matrix.tint.IntMatrix2D;
import cern.jet.random.tdouble.StudentT;
import cern.jet.random.tdouble.engine.DRand;
import eqtlmappingpipeline.metaqtl3.containers.Result... |
5f3b3bbd9c265c65d07d6544d43317a0d788d4a4cfa88983d7ebcfedba472c56 | Java | 29,999 | 659 | /*
* 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 cern.colt.matrix.tdouble.Doubl... |
bba11117cbb95a56d68bf98676645419fd4481b28e39fdd523b4e03c688690bb | Java | 30,518 | 686 | package nl.umcg.deelenp.genotypeharmonizer;
import static JSci.maths.ArrayMath.covariance;
import com.google.common.collect.Lists;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.time.Duration;
import java.time.Instant;
import java.util.ArrayList... |
3c8790f42015412116bcbd85ff6ffff0f1be7cfa632a57ae10bc595e362fa0fe | Java | 30,566 | 1,032 | /** *****************************************************************************
* Copyright (c) 2015 David Lamparter, Daniel Marbach
*
* 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 w... |
03c2339f5f8da996b58b06ce84418cb0131c2ab6b283ff640cc21dfe36daa20c | Java | 30,723 | 877 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.trityper;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.*;
import java.nio.ByteBuffer;
import java.nio.channels.FileChannel;
import java.text.DecimalFormat;
import java.util.... |
39f9a7184694cec2c3dbd9487d0a8280f4addac9539b9aeacaa509db66c457e8 | Java | 30,894 | 968 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import org.apache.commons.math3.util.CombinatoricsUtils;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.containers.Triple;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.util.BaseAnnot;
import umcg.g... |
e762efb5ed28d6157c92febd943ebc9fdbf3d8bf73e8392388b82ac050b93831 | Java | 31,027 | 855 | /*
* @Author: onetism onetism@163.com
* @Date: 2022-08-18 23:08:17
* @LastEditors: onetism onetism@163.com
* @LastEditTime: 2022-08-19 01:25:22
* @FilePath: /MultiGPU_DeconJ_mvn/src/main/java/Zprojection.java
* @Description: 这是默认设置,请设置`customMade`, 打开koroFileHeader查看配置 进行设置: https://github.com/OBKoro1/koro1FileHe... |
bc0bc2917cd7bca43ed9a007398c8e536a2ccce6094698c1192d4fb99ffed038 | Java | 31,083 | 628 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package imputationtool;
import imputationtool.postprocessing.BeagleImputationQuality;
import imputationtool.postprocessing.TriTyperDatasetCorrelator;
import imputationtool.postprocessing.TriTypertoPedMapDatExcludedSNPAn... |
2983ab053ffa285cc662f844bdd3ac26aa0b20821e5abab7a5567b68261de8fd | Java | 31,240 | 792 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.legacy;
//import java.io.*;
//import java.util.*;
//import java.util.concurrent.CompletionService;
//import java.util.concurrent.ExecutorCompletionService;
//import java.util.concurrent.ExecutorSer... |
2d7b71363a4c4b0f35454bb3f00ad359567d62b9b78455f012c2778e5d6e4348 | Java | 31,546 | 941 | /*******************************************************************************
* Copyright (c) 2015 David Lamparter, Daniel Marbach
*
* 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 wi... |
6346a21522102d2a0948066f13da32252c3f42384952d68bd6d8bd04eb032a6f | Java | 31,728 | 1,034 | package network_code_v5.func;
import java.io.*;
import java.util.*;
public class NetworkInteractions
{
public NetworkInteractions(){}
public void removeDuplicatedInputOfGeneNetwork(String networkFolder, String selectedGene)
{
String s = "";
try
{
FileInputStream fis = new FileInputStream(network... |
d28b571bafaf28bacb927aadc10541f4f52e6ff1c1613e3225707e779327fbb3 | Java | 31,904 | 801 | /*
* 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.hash.THash... |
1ab24ad0f00cdd7c9973d6a8191904935bb65b44ddefb4ae5cf9e59681fac1cc | Java | 31,920 | 1,061 | /*-
* #%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... |
ab28b5df03c3b0a31c48a34b60fc3ebf64e58ce06071cc393f7ad73452fe1e6d | Java | 32,594 | 685 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import eqtlmappingpipeline.binarymeta.Main;
import eqtlmappingpipeline.metaqtl3.FDR;
import eqtlmappingpipeline.metaqtl3.FDR.FDRMethod;
import eqtlmappingpipeline.pcaoptimum.PCAOptimum;... |
02a2fde559098e1c94967d3542801e00ad6fdb31b91871a0fa2efc538ffb4f5a | Java | 33,050 | 743 | /*
* 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.QTL;
import eqtlmappingpipeline.metaqtl3.containers.Result;
import eqtlmappingpipeline.metaq... |
ffabc8c0b938488c5723a9f2146495676a9c753ddb3c5d88e6f213d2b4a0a55e | Java | 33,612 | 1,119 | /*
* 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.westrah.binarymetaanalyzer;
import gnu.trove.map.hash.TObjectIntHashMap;
import org.apache.commons.io.FileUtils;
impor... |
9ca8f06f83643ace5c24a44757e707fa9fde9fa54de7a0782a252b0e934ada95 | Java | 33,730 | 741 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.deelenp.genotypeharmonizer;
import java.io.File;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache... |
cea2d25b16eb83289284f56616926db0493438d37cb5e440e386a649e51892ac | Java | 34,048 | 917 | package nl.systemsgenetics.downstreamer.runners;
import cern.colt.function.tdouble.DoubleFunction;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import com.google.common.io.Files;
import com.opencsv.*;
import me.tongfei.progressbar.ProgressBar;
import me.tongfei.progressbar.ProgressBarStyle;
import nl.systemsgenetic... |
fd09cf75247ce8af9bf2b66f0d15497492669bff349d921fbe9cd7582a702c03 | Java | 34,200 | 761 | /*
* 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.pathway;
import cern.colt.matrix.tdouble.DoubleFactory2D;
import cern.colt.matrix.tdouble.Doub... |
7391c67b6fa9e2637d95b3e2d42dd8220491b1800dd83c294f3612ce47a141f4 | Java | 34,426 | 598 | package mbqtl;
import mbqtl.enums.AnalysisType;
import mbqtl.enums.MetaAnalysisMethod;
import mbqtl.enums.PermutationStrategy;
import mbqtl.gfx.QTLDotPlot;
import org.apache.commons.cli.*;
import java.io.IOException;
public class Main {
public static void main(String[] args) {
Options options = new Opt... |
fcc38cea76e9e785d8b4b52bf2ce5e7de94bf1d2cb995ba0a5ee467fbff56487 | Java | 34,492 | 771 | /*
* 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.originalLude;
import java.io.File;
import java.util.HashMap;
import java.util.conc... |
8117b292524c76bb7af5e43d2942a8b09ce9389d02c9c97aece32ffe227434e6 | Java | 35,485 | 811 | /*
* 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 org.molgenis.genotype.bgen;
import java.io.*;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.channels.... |
5e349f947076cd248adabc1bb27d7e5f146043288c7001fc39b8df7052556013 | Java | 36,019 | 699 | /*
* 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.pathway;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.Doubl... |
a40c7ff00916d361a4b098b568d734837228f529da44ae656bbd1d02dab3bea6 | Java | 36,228 | 1,164 | /*-
* #%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... |
6f730a5eb6624293db355022f32fb1be7f5ad294c7df0bbe7aebf9a44f55d9be | Java | 36,817 | 933 | /*
* 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 nl.systemsgenetics.downstreamer.DownstreamerStep3Results;
import nl.systemsgenetics... |
2d6cd02a47f7b63a95049f4b4fe6c05ef58c50d6cfcffae9825692cdebe83785 | Java | 37,590 | 828 | package eqtlmappingpipeline.util;
import eqtlmappingpipeline.metaqtl3.containers.Settings;
import org.apache.commons.configuration.ConfigurationException;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica.io.text.TextFile;
import umcg.g... |
110b570d4652f9d066095854a250c4b6b653b400aa106a3a33ddd7815bc12073 | Java | 37,665 | 888 | package edu.cmu.cs.eyetrack.gui;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
... |
6004d34adf39399405ee04f303d0d9397299f96b2b9a77c62843fc24f412810f | Java | 37,990 | 1,144 | package umcg.genetica.io.binInteraction;
import umcg.genetica.io.binInteraction.gene.BinaryInteractionGene;
import umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantStatic;
import com.google.common.io.CountingInputStream;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.BufferedInputStream;
im... |
2b8f9d360385847911c56ab70cad8ab28601bb2915d4d3f5ff0bf923604c30fe | Java | 38,107 | 1,123 | /*-
* #%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... |
bafe0c2131e991993bc3c38c92ff9989cb921d33f4279fc5041b4fb9498196f3 | Java | 38,188 | 946 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.matrix;
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import ja... |
5c7d98a7db399a076e9a59b4c2f087002374c71041e20d0068e1e67d8c1f239b | Java | 38,478 | 1,124 | /*-
* #%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... |
cc2f0a2dfa0417bf5d584e660c57de0a9b6fbce1b26424b67b2712ef5c179605 | Java | 38,598 | 1,111 | /*-
* #%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... |
623aeb27492cd154a00b8cdce7c63b57a3851f1b17eb81ede97cb0a3e54ce428 | Java | 38,709 | 811 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.binInteraction;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
impo... |
9b3b7626e0a17c0824220492d6f519daa6049032efc2d7b09a6bc254b9d198e9 | Java | 38,996 | 1,116 | /*-
* #%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... |
22d3c023e3a761f8f3d3a6f85f99a8f8584d8584c614f0ab61a3786c3b6e746a | Java | 39,323 | 759 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.deelenp.genotypeharmonizer;
import org.apache.commons.cli.ParseException;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.RandomAccessGenotypeData;... |
0b023496d987de33a43a989ba2d1b47fbea503e7af9666795b2f06bfc3e2f51f | Java | 39,483 | 1,111 | /*-
* #%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... |
cacc4699c450668edc330e3762917fd9965de300ef8a35733e7e3ac64ced7239 | Java | 39,719 | 925 | /*
* 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 com.google.common.collect.Iterables;
import java.io.File;
... |
e782a94e861a00c9da62674ca68eba92ae256cb842d92db65d14d157190a6712 | Java | 39,970 | 1,381 | package umcg.genetica.io.plink;
import umcg.genetica.containers.Pair;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.features.Feature;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.ArrayList;
import jav... |
24bc5a7226a2f61211261fd0729b8dc283ff3866bbb3c8cec680d3aaa6989a99 | Java | 40,640 | 1,135 | /*-
* #%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... |
375ba7bf01caf6ce6d05b7adea0647acfa964c58f256b19d19b792ea70d38b60 | Java | 41,029 | 1,033 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3.containers;
import eqtlmappingpipeline.Main;
import eqtlmappingpipeline.metaqtl3.FDR.FDRMethod;
import gnu.trove.set.hash.THashSet;
import org.apache.commons.configuration.Configurat... |
3c58fe6ef77cec3058d11df538bc7c7ae822ad52082e19badcfbc25ea5444fea | Java | 41,221 | 1,164 | /*-
* #%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... |
5f479a4941b37f00ed9fd33a8302933285f5745306b26d5b14146b2760b8e444 | Java | 42,205 | 1,230 | /*-
* #%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... |
b7d404d6f461af3fd0ca7b420f2c3222afae18103c2f5ed8d38e0d6e086aa401 | Java | 44,099 | 941 | /*
* 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.io.RandomAccessFile;
import java.util.Collections;
import java.util.HashMap;
import java.util.ArrayList;
import ... |
9f56361652b242aa3e7d301bceda4bdf250df603034b4ed75f83503de9ea9514 | Java | 45,239 | 1,016 | package org.molgenis.genotype.vcf;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.*;
import net.sf.samtools.util.BlockCompressedInputStream;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4... |
d577e05263f68042a96cc4d1b76c32b1caaa5a1b1ee2abe0954c3c2121ccad93 | Java | 46,714 | 1,111 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.probemapping;
import gnu.trove.map.hash.THashMap;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputS... |
6898c9ab15ff640cdd31ba58ccfb0ed6bc28c301202086457e01530e90041cdc | Java | 46,825 | 1,052 | package nl.systemsgenetics.genenetworkpathwayenrichment;
import umcg.genetica.containers.Pair;
import umcg.genetica.containers.Triple;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.math.matrix2.DoubleMatrixDatasetRowIterable;
import umcg.genetica.math.stats.Descriptives;
import umcg.genetica.math.stats.... |
40889729c44a32a713770e4effde37dc8d594579d55a8b49e1265f8b240d0888 | Java | 47,443 | 927 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3.graphics;
import cern.colt.matrix.tint.IntMatrix2D;
import umcg.genetica.math.stats.Descriptives;
import eqtlmappingpipeline.metaqtl3.containers.Settings;
import eqtlmappingpipeline.... |
b7c2a54446cc328a239a6e376aeb453e34ba049be8370c10fe1eb4adfd43415c | Java | 47,516 | 940 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.interactionanalysis;
import eqtlmappingpipeline.Main;
import eqtlmappingpipeline.normalization.Normalizer;
import gnu.trove.map.hash.THashMap;
import org.apache.commons.math3.stat.co... |
ab03e596ae3e2c846294fc7d974ed4f65de576cede69cd67fb3b519c566dae0f | Java | 48,192 | 1,036 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.qcpca;
import eqtlmappingpipeline.graphics.ScatterPlot;
import umcg.genetica.math.PCA;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Colle... |
c4754827e25935438c1aa5c9c7547f41b1e6d235312b568892cb48d00130912f | Java | 50,114 | 1,242 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMa... |
0e527c2d1330de9bdc0985eb4d3be620ed371d465b8bd7a074f4f450bb6f7aca | Java | 51,131 | 1,483 | package nl.systemsgenetics.downstreamer.runners;
import cern.colt.GenericPermuting;
import cern.colt.function.tdouble.DoubleDoubleFunction;
import cern.colt.matrix.tdouble.DoubleFactory1D;
import cern.colt.matrix.tdouble.DoubleFactory2D;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.D... |
dbafa1c6a2b71885331e9d1eb1f39f1fee65e5d01d848eb5d651089faede962e | Java | 53,419 | 1,104 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.util;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import umcg.g... |
91e668074582266bc024fecc8826d6168cf0c25b52dc3006c17773209e6e316a | Java | 56,325 | 1,269 | package transeqtlcrossmap;
import java.io.File;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.nio.charset.StandardCharsets;
import java.time.LocalDateTime;
import java.time.format.DateTimeFormatter;
import java.util.*;
import java.util.concurrent.ExecutorService;
import java.uti... |
367b32ae891683bcca2db1754b977f44bde627b8249dbd5e355ebf348f74bf3d | Java | 57,226 | 1,258 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import gnu.trove.map.hash.TDoubleIntHashMap;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.IOException;
import java.util.Arrays;
import java.util.HashMap;
import java.util... |
e713925a74d73eec1ef7ab46b66f3592d8ef51897f199e37896683d8106d3594 | Java | 59,124 | 1,607 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.bin;
/*
* Copyright 1997, University Corporation for Atmospheric Research
* See COPYRIGHT file for copying and redistribution conditions.
*
* RandomAccessFile.java. By Russ Rew, based on
*... |
c1ac2bcbda2299b6cae08dab3f46d41277a454883772fdfb0a0a8eabaaac2fa4 | Java | 59,628 | 1,264 | package mbqtl;
import mbqtl.vcf.DetermineLDVCF;
import mbqtl.vcf.VCFTabix;
import mbqtl.vcf.VCFVariant;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.containers.Pair;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.features.Feature;
import umcg.genetica.io.text.TextFile;
import umcg.geneti... |
ee0d4256acc30ab8d450905029e44a02bdf2002c9428d7ecf3a703b2b2bba692 | Java | 59,896 | 1,281 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseLargeDoubleMatrix2D;
import eqtlm... |
95606a0d4eadb43c1e34b00848a81f3b94e89d107b223ad146a69d1d1470b923 | Java | 62,746 | 1,520 | /*
* 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.eqtlinteractionanalyser.eqtlinteractionanalyser;
import au.com.bytecode.opencsv.CSVReader;
import au.com.by... |
b452a3eb7878514ef59a116207e44bd81e80ba6416e473521d177a7274893084 | Java | 63,049 | 1,676 | /*
* 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;
import edu.emory.mathcs.utils.ConcurrencyUtils;
import htsjdk.tribble.SimpleF... |
ed35d8e475cff60fec47478112df0f93b7045dc385b79fdd7fee852165cc582f | Java | 64,259 | 2,145 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.matrix2;
import cern.colt.matrix.tdouble.DoubleFactory2D;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.algo.D... |
3eec297d9eb169d9ed33ae33bf06a56c7a91338f7fa2e8a3f11f75d435d185bb | Java | 64,339 | 1,272 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import com.itextpdf.text.DocumentException;
import eqtlmappingpipeline.binarymeta.meta.graphics.ZScorePlot;
import eqtlmappingpipeline.graphics.ScatterPlot;
import eqtlmappingpipeline.m... |
01d08ac969f1b0a20117e9eb7f1e0cdbe215674a3af2bcaf2b9ee1a8b04fcb37 | Java | 64,672 | 1,295 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import org.apache.commons.math3.linear.SingularMatrixException;
import org.apache.commons.math3.stat.correlation.SpearmansCorrelation... |
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