sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f81de77eb647ac476c503ca918d43512c7c737b4c932fa029c4ea5d10d30c276 | Java | 13,213 | 268 | package nl.systemsgenetics.downstreamer.io;
import nl.systemsgenetics.downstreamer.runners.options.DownstreamerOptionsDeprecated;
import nl.systemsgenetics.downstreamer.pathway.PathwayAnnotationsFile;
import nl.systemsgenetics.downstreamer.pathway.PathwayDatabase;
import org.apache.commons.lang3.StringUtils;
import or... |
59110f1fec55bff226631161e4e31e3d3f595ebf4c029ebf50ceb2c69a51af72 | Java | 13,254 | 507 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3.containers;
import cern.colt.matrix.tint.IntMatrix2D;
import umcg.genetica.io.trityper.SNP;
import umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset;
import umcg.genetica.io... |
ce38c0bd0927e63145f4f58bdf887e1be69a9b5e85d5118bfb43cc43a720610e | Java | 13,320 | 333 | /*
* 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.apache.commons.math3.excep... |
7b0256ab1b6cc315a243b253707cd16aba29832b0d8006edec0c7ba689dcdbe8 | Java | 13,330 | 280 | package mbqtl;
import mbqtl.datastructures.Dataset;
import mbqtl.stat.BetaDistributionMLE;
import mbqtl.stat.PVal;
import mbqtl.vcf.VCFTabix;
import mbqtl.vcf.VCFVariant;
import umcg.genetica.containers.Triple;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.features.Feature;
import umcg.genetica.features... |
dad3d4a99b4da7da93b6a444412d889bd7634a13c03d4dcbdadc9102b92402a7 | Java | 13,390 | 355 | /*-
* #%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... |
2c1b34b60135443cb9440ee9838a0757412a618d32f95573df3e5c327fc4f1f5 | Java | 13,404 | 353 | /*-
* #%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 ... |
2477f83510f1c497f2d5cb202ef2ca21c7abf73c9e796d9eeff5daa9acbf7413 | Java | 13,445 | 341 |
import ij.*;
import ij.gui.*;
import ij.plugin.*;
import ij.process.*;
public class ImageRectification implements PlugIn{
@Override
public void run(String arg0) {
if (IJ.versionLessThan("1.32c"))
return;
int[] wList = WindowManager.getIDList();
if (wList == null){
... |
d44e7ffba7353c4d4569c8515281b5000bd387c5cd52732c03c34bf74acec555 | Java | 13,449 | 379 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.HashMap;
import java.uti... |
343e58855839117e96fd272cbe7ed223c56fcf376c621d766942ffecd947af4a | Java | 13,471 | 410 | /* Copyright (c) 2019 Thomas Braschler <thomas.braschler@unige.ch>
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or
## (at your option) any later version... |
acbe08623b87e9af4532d1cfd590f32e55479d15c864fc1aa291c9940874daab | Java | 13,582 | 439 | package nl.systemsgenetics.benchmark;
import nl.systemsgenetics.simplegeneticriskscorecalculator.Main;
import org.apache.commons.cli.*;
import org.apache.commons.math3.stat.correlation.PearsonsCorrelation;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.SNP;
import... |
0dc80ab536aeb42c479eaef29bf51f428fdb18b7780e7a9984d511239bbe9921 | Java | 13,628 | 407 | /*
* SymmetricByteDistancaMatrix.java
*
* Created on 04 June 2004, 15:53
*/
package umcg.genetica.math.matrix;
/**
*
* Symmetric Byte Distance Matrix: A memory efficient matrix capable of performing calculations on all genes x all genes:
*
* @author Lude Franke
*/
public class SymmetricByteDistanceMatrix {
... |
e48632b22ab50c5687b4988c24a94f5ed6f5f17e98751ce0f2be216f0ba5a016 | Java | 13,658 | 395 | /*-
* #%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... |
3172ff97399b9a6c97322702409575b1997b134315b22552e15bf1e5fdbcb028 | Java | 13,662 | 380 | package mbqtl;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.QTLTextFile;
import umcg.genetica.io.trityper.util.ChrAnnotation;
import umcg.genetica.text.Strings;
import java.io.File;
import java.io.IOException;
import java.util.*;
public class QTLFileSorter {
... |
5be6a4eb6a0ecce977f2ed1a0909e4b471685e62889951de62fed34ce27bc2ab | Java | 13,663 | 337 | package org.molgenis.genotype.modifiable;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.molgenis.genotype.AbstractRandomAccessGenotypeData;
import org.molgenis.genotype.Allel... |
a40c97a73388bb8d4d3ef1d3665b4ea6cab3645957297754a5d913d9ca06090f | Java | 13,755 | 473 | /*-
* #%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... |
9f9b2f27e03f01103e17c9dc6e30f9f5f7759d5a2cc1c9ad88e34b026e7c7e63 | Java | 13,780 | 388 | /*-
* #%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... |
5823396e9e9b67370c245cc18e3ec625b74ba99e067945b1764a453cc7786a20 | Java | 13,825 | 343 | /*
* 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.datg;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import com.opencsv.CSVWriter;
import gnu.trove.list.a... |
397e03bd201dc369f103e7f0a375eb6064142de9fbbd71f15829aae2a509b9cb | Java | 13,850 | 375 | /*-
* #%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... |
6db17bcba4d827f236d316f7d98581b21e0b00b14e168449c4c727ac3754a18f | Java | 13,933 | 481 | /*-
* #%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... |
517ba3bf672b1cbc0e361cc9c4fc1f01f3c69e13c77fa1d6b7888d9bf7eb14d9 | Java | 13,948 | 534 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.text;
import net.jpountz.lz4.LZ4BlockInputStream;
import net.jpountz.lz4.LZ4BlockOutputStream;
import umcg.genetica.containers.Pair;
import umcg.genetica.containers.Triple;
import umcg.genetica.... |
46d6da05c420dc42389e67dca6d68f6761cdf6b5b2339842a8b4663b2e810e80 | Java | 13,958 | 390 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import au.com.bytecode.opencsv.CSVReader;
import au.com.bytecode.opencsv.CSVWriter;
import java.io.F... |
4920805ce0afb6c339dac6092cfec037f4c8b4ed2d8d6bfff518b264b00e7fa9 | Java | 13,999 | 363 | package transeqtlcrossmap;
import java.io.File;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Set;
import net.sf.picard.reference.FastaSequenceFile... |
89ed3f82e487e5a75f05ec1bcc25145066b7bc0e4eebed819db1c4d5afffd921 | Java | 14,057 | 437 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatrix2D;
import com.opencsv.CSVParser;
import com.opencsv.C... |
295c99550179f6b513df7026c10f6bee9d36e2963121000e43ac4bff0f0018bc | Java | 14,072 | 505 | /*******************************************************************************
* 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... |
bcd0b088d2f1663df38a0a34c21a89451ac2ab7594166621919696d21e2ac4a9 | Java | 14,120 | 499 | /*-
* #%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... |
45d91d924ebe6dcfee2b1c39f918c3eec925f739b15c80e41f4912c5f3ec0391 | Java | 14,184 | 295 | package nl.systemsgenetics.downstreamer.runners;
import cern.colt.list.tdouble.DoubleArrayList;
import cern.colt.list.tint.IntArrayList;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import me.tongfei.progressbar.ProgressBar;
import me.tongfei.progressbar.ProgressBarStyle;
import nl.systemsgenetics.downstreamer.io.I... |
6e458bfcfb2743e2b274f0775c3a27091db1e8c6bc66746d27f5aa24ed9ecfa6 | Java | 14,201 | 413 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.plink;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.... |
40eadf473e42c6408d9c3eabb306e9fc875231680cacc83d8720ec97b1579e27 | Java | 14,350 | 417 | /*
* 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.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.HashMap;
import java.util.H... |
7c143b63646a2dbe2b9da36f3d26dae04fd100563502f63ac036452d7e23772c | Java | 14,351 | 354 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatrix1D;
import com.opencsv.CSVWriter;
import gnu.trove.lis... |
4d35225acd28b684a10f9e0d67f46ebffc129d043ab3764aca3d516f83a1545b | Java | 14,355 | 443 | /*-
* #%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... |
f5f0106add50714037a72f79514217f2f76cc73b15b4d774bdb8769b78fe8dfd | Java | 14,492 | 342 | /*
* 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.IOException;
import java.io.PrintWriter;
import ja... |
4d8208665bb4ba173b08e06411114fe7989fc60f423b0a751e4b10c2a5bf4ff6 | Java | 14,533 | 406 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper;
import gnu.trove.map.hash.THashMap;
import gnu.trove.set.hash.THashSet;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
... |
79ffca856834e976e0048ec229cd0686ed1f9e2376300f1bca22de4b43eef134 | Java | 14,598 | 285 | package test.java.decon_eQTL;
import main.java.decon_eQTL.CommandLineOptions;
import main.java.decon_eQTL.Deconvolution;
import main.java.decon_eQTL.DeconvolutionResult;
import main.java.decon_eQTL.Main;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.LineIterator;
import org.hamcrest.CoreMatchers... |
45d7dd09ca6c9569b16197a3447f2d1d3cb9876f3cc071669266af1f48be4423 | Java | 14,615 | 469 | package org.molgenis.genotype.oxford;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.RandomAccessFile;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.L... |
2bfae9f4315a90e08ef208abd7ae3f194c753d79751db090f467a462bfbd6523 | Java | 14,630 | 404 | /*
* 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 java.io.*;
import java.util.*;
import java.util.zip.GZIPInputStream;
import c... |
8f342550c3966754473aaa84f2a7bbd5da10dea65e094c67fa382a6ab36a5a81 | Java | 14,783 | 507 | /*-
* #%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... |
12aaef30ec4d4adbc5c8decd73265517f66a14de90fdcc022e2b3ad4a3bdb303 | Java | 14,787 | 396 | package org.molgenis.genotype;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.HashSet;
... |
a342ca1be65f1b6f60c2ad3b82c155079c8b0f2fc86e525365b108b36e6b4741 | Java | 14,849 | 517 | /*******************************************************************************
* 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... |
c52b645d2a05e5cf24613639e1328dca0a961146601982f1f8b06cfaa1de0918 | Java | 14,850 | 327 | package ebi.spot.neo4j2owl.exporter;
import ebi.spot.neo4j2owl.N2OException;
import ebi.spot.neo4j2owl.N2OLog;
import ebi.spot.neo4j2owl.N2OStatic;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import org.neo4j.graphdb.GraphDatabaseService;
import org.neo4j.graphdb.QueryExecutio... |
ffefaa0b0e7e3e6d0ba79953e2f49eba62df7a4a2bbacc8333a9474e98d61855 | Java | 14,856 | 420 | /*-
* #%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 ... |
aa9227e77c8f05b515cfefb9248a27ca4f420cd4e6c9bc384a6c0fed6b3f27a2 | Java | 14,857 | 325 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.File;
import java.io.IOExce... |
7de0ab6429c5058b0131472481f4ebe2d9ac210255b5b6f36dd2412c156e8682 | Java | 14,935 | 427 | package umcg.genetica.graphics.panels;
import umcg.genetica.containers.Pair;
import umcg.genetica.features.Feature;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import umcg.genetica.graphics.themes.DefaultTheme;
import java.awt.*;
import java.text.DecimalFormat;
import java.util... |
fecb6c58876c3bbae2eb39429d5abab8a1d8518a5944eb7e009ac3f7ac2883c6 | Java | 14,942 | 430 | /*-
* #%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 ... |
3adbe0823dd101bcb4f367ea5234f3c9ca212ce3e5843833cabc7ba75ece21cb | Java | 14,948 | 444 | package umcg.genetica.graphics.panels;
import umcg.genetica.containers.Pair;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import umcg.genetica.math.stats.Correlation;
import umcg.genetica.math.stats.Regression;
import umcg.genetica.util.Primitives;
import java.awt.*;
import java... |
3bb83a3c853378676be4ad126b6beaa98c0d6b7d101c2f3e1e85840aeeb20f52 | Java | 14,994 | 418 | /*-
* #%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... |
5db54791fef5665eb47ad86dddb858dfabe28a8fd7fcee1247c4200a8f12ea75 | Java | 15,005 | 423 | /*
* 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.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util... |
e87116e2460da70110cb7c794ac32b8308adfad179766294ad148d8514890e44 | Java | 15,020 | 368 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.trityper;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.molgenis.genotype.Alleles;
i... |
03a4ba46693233d1da33622d339582043b49bc2f80ff9ae40bed71a095141de7 | Java | 15,044 | 413 | /*
* 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 umcg.genetica.io.Gpio;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica... |
961d69e2536e52ae9378243be82bf5917e985dc182c5c18904a16e0add8caaf7 | Java | 15,052 | 441 | package nl.systemsgenetics.downstreamer;
import nl.systemsgenetics.downstreamer.runners.PreparePermutations;
import nl.systemsgenetics.downstreamer.io.ExcelWriter;
import nl.systemsgenetics.downstreamer.pathway.PredictedPathwayAnnotations;
import nl.systemsgenetics.downstreamer.runners.options.*;
import nl.systemsgene... |
01c3585ba968e13b76549532e1a6a7177825defa27bac676f26af56fa75ac089 | Java | 15,083 | 369 | /*-
* #%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... |
71e3d85eff6dd3d28a6d4dccfdb1cf68f116abba45fb2e657a4e8a61f61f83a5 | Java | 15,097 | 405 | /*
* 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 com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com... |
f9dd43b6e237fd459b9a4c3996ef4194363c0ff39df57c779b726222f0348139 | Java | 15,101 | 322 | package mbqtl;
import mbqtl.datastructures.Dataset;
import mbqtl.vcf.VCFTabix;
import mbqtl.vcf.VCFVariant;
import umcg.genetica.containers.Triple;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.features.Feature;
import umcg.genetica.features.Gene;
import umcg.genetica.io.text.TextFile;
import umcg.geneti... |
3cb6d11bf52febb3c56c3d1a9898de3e7fb37ea09033fddd8521e00649689a6b | Java | 15,121 | 359 | package nl.systemsgenetics.downstreamer.runners;
import nl.systemsgenetics.downstreamer.DownstreamerStep3Results;
import nl.systemsgenetics.downstreamer.DownstreamerStep2Results;
import nl.systemsgenetics.downstreamer.runners.options.DownstreamerMode;
import nl.systemsgenetics.downstreamer.DownstreamerStep1Results;
im... |
577c505800b8d093146f952a294c8184623babb9612fad0dd482207a3f5f4222 | Java | 15,157 | 448 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.oxford;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.RandomAccessFile;
import java.util.ArrayList;
import java.util.Collections;
imp... |
015050237082b7dddb6a7ef0388fca1c27488d413830e35111178f6a402d316e | Java | 15,202 | 307 | /*
* 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.interactionanalysis;
import java.awt.Color;
import java.io.IOException;
import java.text.DecimalFormat;
im... |
9103ddd481356ed314a884e78fae6612ce0e8cc313e09060f29d6d902ad09eaa | Java | 15,213 | 480 | /*-
* #%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... |
f06b77772669e6f1963ee489c10aa29269dcab66af68551fe284fb566eee2b25 | Java | 15,267 | 481 | package org.molgenis.genotype.modifiable;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.mo... |
1ea6a80c572b4ed89bf180ba8cb2420bbe32d24eca6a986321706e01c2f8daf8 | Java | 15,272 | 405 | /*
* 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.Arrays;
import java.util.HashSet;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.io.... |
30a547f44f5ce73f5656b46a7a26111c51c2b32fdbe3afe2141d69c0511df59e | Java | 15,289 | 502 | /*-
* #%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... |
25247bece3fd68fa1ccd30bb7b166c12aa3acb06c9761ea5c67f56a9bd18fa62 | Java | 15,292 | 397 | /*-
* #%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... |
8e1f1b955e4272ccdd71c41b536ffc41b08657528ddfb0cc9c6f597278641edc | Java | 15,304 | 533 | /*-
* #%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... |
6ba7fe77bd47cdcdb9cbce963d8a61f85bc0def9eafc06d03e8d9c77e82aaa1a | Java | 15,323 | 437 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io... |
5c1dc2f27e06f7114528ee31c6dfeacf3bcab8768f49c8abc21622037c9e15be | Java | 15,353 | 359 | /*
* 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 java.io.*;
import org.apache.commons.cli.*;
import... |
22e9fcfb646b9f96ff292c352833b6852be11c3bf3e4b6b785526670bd286900 | Java | 15,358 | 506 | /*-
* #%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... |
0f3cdce2c0fc77b26448514e48b39c0f80e2f8ed9f69502b00eabe03afdc644b | Java | 15,373 | 429 | /*
* 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.apache.commons.math3.distr... |
d10a0b994976e60ae4d9c812642c6c5b60ea5564305c5085aa72705e379ef468 | Java | 15,381 | 421 | package eqtlmappingpipeline.interactionanalysis;
import au.com.bytecode.opencsv.CSVReader;
import au.com.bytecode.opencsv.CSVWriter;
import gnu.trove.list.array.TDoubleArrayList;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOExcept... |
b710990e363da7a1f2720256050241046438fc8353a909b2ef191d004eb914cb | Java | 15,383 | 529 | /*******************************************************************************
* 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... |
58d6e53258db748771926dfd95b1e3eebcb19eae1931a68fa7a3b1ebe47c8dc7 | Java | 15,408 | 416 | /*-
* #%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... |
acc8c8a05ef121e04725af7fc2cf99fcb1f9a5f7a4e4020d589a3d16af15c47f | Java | 15,413 | 532 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta;
import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuration.XMLConfiguration;
import java.util.ArrayList;
import java.util.loggin... |
0d35ff3ba36f568072596d4a7c80a26ba65354bd25b76247d72b8f26d00343ef | Java | 15,462 | 453 | /*-
* #%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... |
6fd1b5464d760b0a76859f8d8214dfecabc7713db01e8f371904c7d88e7c956a | Java | 15,544 | 389 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.graphics;
import JSci.maths.ArrayMath;
import com.itextpdf.text.DocumentException;
import com.itextpdf.text.Rectangle;
import java.awt.Color;
import java.awt.Font;
import java.awt.FontMetrics;
impo... |
8c6035e22cd60ccce9805dfde2bd30439a28e1fdd5c1764e51daa2c676856fe2 | Java | 15,562 | 359 | /*
* 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 eqtlmappingpipeline.meta... |
2308fb964176caa0cd0ee36b3a0208a0427e24901f855ff152891ca8df2a563b | Java | 15,571 | 359 | /*-
* #%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... |
9d957de33028e8c121d437af3f7962170083f485149cc2d38344a7fa1e0a571c | Java | 15,571 | 359 | /*-
* #%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... |
e06c8d51f8629016dce68ef51565806d9db47573f19b3e89990b7897dfce5a63 | Java | 15,583 | 412 | /*
* 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... |
cda47bbb090c1d191f48bea46d86351cdaeafe930a7372d55c8fc9fd9d05a4cb | Java | 15,618 | 397 | /*-
* #%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... |
97dd2ee609fa9fef31a9fb2bd6c8ff7e0f4be96ddf1ffd0fd5ac197fed5432ca | Java | 15,665 | 409 | /*-
* #%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... |
4933d943af1050988db76dabdf8ee9da58cd9fd4cb8cb568b6070b3de749eec1 | Java | 15,701 | 374 | /*
* 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 java.util.Arrays;
import org.a... |
4840ead74ce2b15f1db8e7ba0dab9d74570d250656ce5db4fb31069bb69035bc | Java | 15,706 | 449 | /*-
* #%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... |
4f1949039fa84735417fac29f9052d2127bb71bc29f63fa006a78b608cd60ded | Java | 15,709 | 452 | package nl.umcg.westrah.binarymetaanalyzer;
import gnu.trove.map.hash.THashMap;
import gnu.trove.map.hash.TObjectIntHashMap;
import org.apache.commons.collections.primitives.ArrayIntList;
import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
import org.apache.commons.math3.stat.descriptive.SummarySta... |
695a8a3216f2f93b7ba2c4f3af08230ac8afc325d3d72686e06551bf103d5238 | Java | 15,757 | 425 | /*-
* #%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... |
4e27727abc71c737f1188e270f86ee0d1b3babf91fb3bb4da667fbe6bd2d8907 | Java | 15,844 | 493 |
package umcg.genetica.genomicboundaries;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.... |
7cb52739bf2a1fe60ae833cc701c0de79ecc9d167cd8fcc20890709c0849e848 | Java | 15,899 | 520 | /*-
* #%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... |
af29ab644607f9cf29e5fb321351c033ac5243aea8a4d567ecd094292da7da9a | Java | 15,920 | 455 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import au.com.bytecode.opencsv.CSVReader;
import au.com.bytecode.opencsv.CSVWriter;
import java.io.F... |
19812a564ab700d0fcfbeb8158b1becdf318fea9206e9d749023a3c96e19fe9e | Java | 15,925 | 456 | package umcg.genetica.io.binInteraction;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.BufferedOutputStream;
import java.io.DataOutputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.RandomAccessFile;
import jav... |
773c5274cde85c5ab1a3e74fe5c28353063e71619e4907f0bde6d5e675556575 | Java | 15,958 | 366 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
import eqtlmappingpipeline.normalization.Normalizer;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Lis... |
08fa80ef317d478bc611eae7e4332ef300daff7d518fbb2b20412c55bdace755 | Java | 15,972 | 436 | package nl.systemsgenetics.genenetworkpathwayenrichment;
import org.apache.commons.math3.distribution.TDistribution;
import umcg.genetica.containers.Pair;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.math.stats.Descriptives;
import umcg.genetica.math.stats.FisherExactTest;
import umcg.genetica.math.stat... |
4c7d417e2c3689feab87b503ba690e9c9e325dfa0ae3de3845b00d7978f76b2a | Java | 16,039 | 426 | /*
* 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.hpo;
import umcg.genetica.io.hpo.HpoOntology;
import cern.colt.matrix.tdouble.DoubleMatr... |
2a7683d181fa588438a9b1d094dd9d33b4c36b9b9410b7c6c43ce551065e59ea | Java | 16,102 | 446 | /*-
* #%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... |
a45d99d5c7fb8209917148425c35dc62158203c967f788acc713a90c1aed3dba | Java | 16,118 | 402 | package nl.systemsgenetics.downstreamer.summarystatistic;
import nl.systemsgenetics.downstreamer.summarystatistic.filters.PvalueFilterSmaller;
import nl.systemsgenetics.downstreamer.summarystatistic.filters.RegionFilter;
import nl.systemsgenetics.downstreamer.summarystatistic.filters.SummaryStatisticsRecordFilter;
im... |
2428c276211ed8e1a85c9146cf01ba717dc37539f639c6c912de2b8fa550b15d | Java | 16,139 | 529 | /*-
* #%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... |
03c7fa83a762cd2931341696411c917f806bb62b1ca64479f51fe577df1ddda2 | Java | 16,153 | 407 | /*-
* #%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... |
ce196d7070480bb645f36d093c44ced9f1856d3ed6624299c345f7e382b0b180 | Java | 16,155 | 400 | package org.molgenis.genotype.vcf;
import java.io.File;
import java.io.IOException;
import java.net.URISyntaxException;
import java.nio.file.Paths;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.*;
import org.apache.commons.io.FilenameUtils;
import org.molgenis.genotype.*;
import org... |
fcb06e59b2c2f2f2d1937c4b9915e3d32b17b363bc95b9590a340d3ed61490f2 | Java | 16,209 | 424 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.interactionanalysis;
import cern.jet.random.tdouble.StudentT;
import org.apache.commons.math3.linear.SingularMatrixException;
import org.apache.commons.math3.stat.regression.OLSMultipleLinear... |
3f3cb0caea3877fba53550a4f7017021cc0dfe144730b88359b66e5c56c2e7b2 | Java | 16,275 | 441 | package mbqtl.gfx;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import umcg.genetica.graphics.panels.Panel;
import umcg.genetica.graphics.themes.DefaultTheme;
import java.awt.*;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Collections;
import java... |
f4fb5ff4d3ef865beabf9ae317e036e27cabef81fc9c8a1e102c9d805d27c4b4 | Java | 16,390 | 504 | /*-
* #%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... |
b1b167a99609fb0556d956bd64b73fda836478cf0aede48e489ee1623c02a6af | Java | 16,391 | 450 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import JSci.maths.statistics.NormalDistribution;
import cern.jet.random.tdouble.StudentT;
import cern.jet.stat.tdouble.Probability;
import java.util.ArrayList;
//import cern.jet.rando... |
d0f806475f363f03ed528398696cae18b226fcf4a31e2c8ba024fa961d8adf44 | Java | 16,426 | 413 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.matrix2;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D;
import cern.colt.matrix.tdoub... |
e48a9d40bfc335fda5384a471dd1a05ddfbb9d77b41e5da7f1db52d48397531b | Java | 16,481 | 402 | package org.molgenis.genotype;
import org.molgenis.genotype.bgen.BgenGenotypeData;
import org.molgenis.genotype.multipart.IncompatibleMultiPartGenotypeDataException;
import org.molgenis.genotype.multipart.MultiPartGenotypeData;
import org.molgenis.genotype.oxford.GenGenotypeData;
import org.molgenis.genotype.oxford.Ha... |
2da32e0c928e1e1030efb128ff80eb39afeeb0f19bf822c5cafdafd8171cb457 | Java | 16,490 | 435 | /*-
* #%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... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.