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Query based tools in BACNET
In this tutorial, we will explain how-to use BACNET architecture to make query-base multi-omics analysis.
We have added a test function which is ran when the BannerView loaded. Open ''bacnet.e4.rap.TestPart.java'' -> go to runTests() function, and add
System.out.println("test run");
When running "bacnet.e4.rap", you will see ''test run'' displayed in the console.
Here are a list of BACNET script to add in runTests() to browse ListeriomicsSample database.
(If you need help for BACNET API go on the JavaDoc)
- How-to get List of genomes?
- How-to get List of transcriptomes?
- How-to get List of proteomes?
- How-to get list of genes and ncRNA?
- How-to search gene and print available information?
- How-to search gene and print its sequences?
- How-to search gene and print its homologs?
- How-to search gene and relevant omics datasets?
- How-to show expression of gene in different omics dataset?
- How-to correlate omics datasets?
- How-to load table and add annotation?
- How-to display omics dataset on GenomeViewer?
ArrayList<String> genomes = Genome.getAvailableGenomes();
for(String genome : genomes) {
System.out.println(genome);
}
Expected output with ListeriomicsSample
Listeria monocytogenes EGD-e
Listeria monocytogenes EGD
Listeria monocytogenes 10403S
ArrayList<BioCondition> bioconditions = BioCondition.getAllBioConditions();
for(BioCondition biocond : bioconditions) {
System.out.println(biocond.getName() +" "+ biocond.getGenomeName() +" "+ biocond.getTypeDataContained());
}
Expected output with ListeriomicsSample
BHI_2014_EGDe Listeria monocytogenes EGD-e [RNASeq]
CellWall_2004_EGDe Listeria monocytogenes EGD-e [Proteome]
EGD_WT Listeria monocytogenes EGD-e [GeneExpr, Tiling]
EGDe_280212 Listeria monocytogenes EGD-e [GeneExpr, Tiling]
EGDe_30C Listeria monocytogenes EGD-e [TSS]
EGDe_37C_RiboSeq Listeria monocytogenes EGD-e [RiboSeq]
EGDe_37C_TSS Listeria monocytogenes EGD-e [TSS]
EGDe_37C_TermSeq Listeria monocytogenes EGD-e [TermSeq]
Exoproteome_2010_EGDe Listeria monocytogenes EGD-e [Proteome]
Extracellular_BHI_2011_EGDe Listeria monocytogenes EGD-e [Proteome]
Extracellular_UGiessen_2010 Listeria monocytogenes EGD-e [ExpressionMatrix]
IFN_Intracellular_UGiessen_2010 Listeria monocytogenes EGD-e [ExpressionMatrix]
Intracellular_UGiessen_2010 Listeria monocytogenes EGD-e [ExpressionMatrix]
Macrophages_2014_EGDe Listeria monocytogenes EGD-e [RNASeq]
Stat_2009_EGDe Listeria monocytogenes EGD-e [Proteome]
prfA_Star Listeria monocytogenes EGD-e [GeneExpr, Tiling]
ArrayList<BioCondition> bioconditions = BioCondition.getAllBioConditions();
for(BioCondition biocond : bioconditions) {
for(OmicsData omics : biocond.getTranscriptomesData()){
System.out.println(biocond.getGenomeName() + " " + omics.getName());
}
}
Expected output with ListeriomicsSample
Listeria monocytogenes EGD-e BHI_2014_EGDe_f
Listeria monocytogenes EGD-e BHI_2014_EGDe_r
Listeria monocytogenes EGD-e EGD_WT.ge
Listeria monocytogenes EGD-e EGD_WT.+.gr
Listeria monocytogenes EGD-e EGD_WT.-.gr
Listeria monocytogenes EGD-e EGDe_280212.ge
Listeria monocytogenes EGD-e EGDe_280212.+.gr
Listeria monocytogenes EGD-e EGDe_280212.-.gr
Listeria monocytogenes EGD-e EGDe_30C_f
Listeria monocytogenes EGD-e EGDe_30C_r
Listeria monocytogenes EGD-e EGDe_37C_RiboSeq_f
Listeria monocytogenes EGD-e EGDe_37C_RiboSeq_r
Listeria monocytogenes EGD-e EGDe_37C_TSS_f
Listeria monocytogenes EGD-e EGDe_37C_TSS_r
Listeria monocytogenes EGD-e EGDe_37C_TermSeq_f
Listeria monocytogenes EGD-e EGDe_37C_TermSeq_r
Listeria monocytogenes EGD-e Macrophages_2014_EGDe_f
Listeria monocytogenes EGD-e Macrophages_2014_EGDe_r
Listeria monocytogenes EGD-e prfA_Star.ge
Listeria monocytogenes EGD-e prfA_Star.+.gr
Listeria monocytogenes EGD-e prfA_Star.-.gr
ArrayList<BioCondition> bioconditions = BioCondition.getAllBioConditions();
for(BioCondition biocond : bioconditions) {
for(OmicsData omics : biocond.getProteomicsData()){
System.out.println(biocond.getGenomeName() + " " + omics.getName());
}
}
Expected output with ListeriomicsSample
Listeria monocytogenes EGD-e CellWall_2004_EGDe
Listeria monocytogenes EGD-e Exoproteome_2010_EGDe
Listeria monocytogenes EGD-e Extracellular_BHI_2011_EGDe
Listeria monocytogenes EGD-e Stat_2009_EGDe
Search them in a genome (ex: Listeria monocytogenes EGD-e)
// get genome
String genomeName = Genome.EGDE_NAME;
System.out.println("Open: "+genomeName);
Genome genome = Genome.loadGenome(genomeName);
// get list of genes and print all
LinkedHashMap<String, Gene> genes = genome.getGenes();
for(String geneName : genes.keySet()) {
Gene gene = genes.get(geneName);
System.out.println(gene + " ("+gene.getGeneName()+")");
}
// get list of ncRNA
LinkedHashMap<String, NcRNA> ncrnas = genome.getNcRNAs();
for(String ncrnaName : ncrnas.keySet()) {
NcRNA ncrna = ncrnas.get(ncrnaName);
System.out.println(ncrna + " ("+ncrna.getGeneName()+")");
}
Expected output with ListeriomicsSample
Open: Listeria monocytogenes EGD-e
Load Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1_genomic.fna
Number of chromosomes found 1
lmo0001 318 1673 1356 + (dnaA)
lmo0002 1867 3012 1146 + (dnaN)
lmo0003 3121 4464 1344 + ()
lmo0004 4644 4865 222 + ()
lmo0005 4869 5981 1113 + (recF)
lmo0006 6030 7970 1941 + (gyrB)
lmo0007 8065 10593 2529 + (gyrA)
lmo0008 10728 12242 1515 + ()
lmo0009 12258 12776 519 + ()
lmo0010 12918 13886 969 + ()
........
lmot01 82705 82777 73 + ()
lmor01 237466 239020 1555 + ()
lmor02 239265 242195 2931 + ()
lmor03 242276 242385 110 + ()
........
String geneName = "lmo0200";
String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);
// search gene
Gene gene = genome.getGeneFromName(geneName);
// print general information
System.out.println(gene + " " + gene.getInfo());
Expected output with ListeriomicsSample
Load Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1_genomic.fna
Number of chromosomes found 1
lmo0200 203640 204353 714 - prfA, listeriolysin positive regulatory protein
(DNA and AA)
String geneName = "lmo0200";
String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);
// search gene
Gene gene = genome.getGeneFromName(geneName);
// print gene nucleotide sequence
System.out.println(gene.getSequence());
// print gene amino acid sequence
System.out.println(gene.getSequenceAA());
Expected output with ListeriomicsSample
Load Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1_genomic.fna
Number of chromosomes found 1
ATGAACGCTCAAGCAGAAGAATTCAAAAAATATTTAGAAACTAACGGGATAAAACCAAAACAATTTCATAAAAAAGAACTTATTTTTAACCAATGGGATCCACAAGAATATTGTATTTTTCTATATGATGGTATCACAAAGCTCACGAGTATTAGCGAGAACGGGACCATCATGAATTTACAATACTACAAAGGGGCTTTCGTTATAATGTCTGGCTTTATTGATACAGAAACATCGGTTGGCTATTATAATTTAGAAGTCATTAGCGAGCAGGCTACCGCATACGTTATCAAAATAAACGAACTAAAAGAACTACTGAGCAAAAATCTTACGCACTTTTTCTATGTTTTCCAAACCCTACAAAAACAAGTTTCATACAGTCTAGCTAAATTTAATGATTTTTCGATTAACGGGAAGCTTGGCTCTATTTGCGGTCAACTTTTAATCCTGACCTATGTGTATGGTAAAGAAACTCCTGATGGCATCAAGATTACACTGGATAATTTAACAATGCAGGAGTTAGGATATTCAAGTGGCATCGCACATAGCTCAGCTGTTAGCAGAATTATTTCCAAATTAAAGCAAGAGAAAGTTATCGTGTATAAAAATTCATGCTTTTATGTACAAAATCTTGATTATCTCAAAAGATATGCCCCTAAATTAGATGAATGGTTTTATTTAGCATGTCCTGCTACTTGGGGAAAATTAAATTAA
MNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN
Print result as fasta file
String geneName = "lmo0200";
String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);
// search gene
Gene gene = genome.getGeneFromName(geneName);
ArrayList<String> listResults = new ArrayList<String>();
// go trough all homologs
for(String genomeNameHomolog : gene.getConservationHashMap().keySet()) {
Genome genomeHomolog = Genome.loadGenome(genomeNameHomolog);
String homologInfo = gene.getConservationHashMap().get(genomeNameHomolog);
String genehomologName = homologInfo.split(";")[0];
String similarity = homologInfo.split(";")[2];
Gene genehomolog = genomeHomolog.getGeneFromName(genehomologName);
listResults.add("> "+ genehomologName + " - "+genomeNameHomolog + " - similarity="+similarity);
listResults.add(genehomolog.getSequenceAA());
}
for(String result : listResults) {
System.out.println(result);
}
Expected output with ListeriomicsSample
Load Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1_genomic.fna
Number of chromosomes found 1
Load Listeria monocytogenes EGD
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD/GCF_000582845.1_SV_1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD/GCF_000582845.1_SV_1_genomic.fna
Number of chromosomes found 1
Load Listeria monocytogenes 10403S
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes 10403S/GCF_000168695.2_ASM16869v2_genomic.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes 10403S/GCF_000168695.2_ASM16869v2.fna
Number of chromosomes found 1
> lmo0200 - Listeria monocytogenes EGD-e - similarity=1.0
MNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN
> LMON_RS00965 - Listeria monocytogenes EGD - similarity=0.9915612
MNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICSQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLAYPATWGKLN
> LMRG_RS00965 - Listeria monocytogenes 10403S - similarity=1.0
MNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN
Get transcriptomes and proteomes in which the gene is found.
String geneName = "lmo0200";
String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);
// search gene
Gene gene = genome.getGeneFromName(geneName);
// get transcriptomics datasets
double cutoffLogFC = GenomeElementAtlas.DEFAULT_LOGFC_CUTOFF;
Filter filter = new Filter();
filter.setCutOff1(cutoffLogFC);
GenomeElementAtlas atlas = new GenomeElementAtlas(gene, filter);
System.out.println("Over expressed in " + atlas.getOverBioConds().size() + " transcriptomic datasets");
for(String bioCond : atlas.getOverBioConds()) {
System.out.println(bioCond);
}
System.out.println("Under expressed in " + atlas.getUnderBioConds().size() + " transcriptomic datasets");
// Print datasets over expressed
for(String bioCond : atlas.getUnderBioConds()) {
System.out.println(bioCond);
}
System.out.println("Not diff expressed in " + atlas.getNotDiffExpresseds().size() + " transcriptomic datasets");
for(String bioCond : atlas.getNotDiffExpresseds()) {
System.out.println(bioCond);
}
// get proteomics datasets
ExpressionMatrix exprProteomesMatrix = Database.getInstance().getExprProteomesTable(genomeName);
System.out.println(gene.getName());
if (exprProteomesMatrix.getRowNames().containsKey(gene.getName())) {
for (String header : exprProteomesMatrix.getHeaders()) {
double value = exprProteomesMatrix.getValue(gene.getName(), header);
if (value > 0) {
System.out.println("Found in " + header + " proteome");
}
}
}
Expected output with ListeriomicsSample
Load Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1.fna
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Genomes/Listeria monocytogenes EGD-e/GCF_000196035.1_ASM19603v1_genomic.fna
Number of chromosomes found 1
Listeria monocytogenes EGD-e
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Transcriptomes/Table_LOGFC_Listeria monocytogenes EGD-e
Over expressed in 2 transcriptomic datasets
EGD_WT vs EGDe_280212
prfA_Star vs EGDe_280212
Under expressed in 3 transcriptomic datasets
Extracellular_UGiessen_2010 vs IFN_Intracellular_UGiessen_2010
Extracellular_UGiessen_2010 vs Intracellular_UGiessen_2010
Macrophages_2014_EGDe vs BHI_2014_EGDe
Not diff expressed in 0 transcriptomic datasets
/Users/christophebecavin/Documents/BACNET/ListeriomicsSample/Database/Proteomes/Table_Expr_Listeria monocytogenes EGD-e
lmo0200
Found in Stat_2009_EGDe proteome
String geneName = "lmo0196";
String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);
// search gene
Gene gene = genome.getGeneFromName(geneName);
/*
* Select some datasets
*/
ArrayList<String> bioConditions = new ArrayList<>();
bioConditions.add("BHI_2014_EGDe"); // RNASeq data
bioConditions.add("EGDe_280212"); // Tiling array data
bioConditions.add("Extracellular_BHI_2011_EGDe"); // proteomics data
/*
* Load all datasets (Load absolute expression values)
* Modified from: bacnet.genomeBrowser.core.DataTrack.loadData()
*/
ArrayList<OmicsData> omics = new ArrayList<OmicsData>();
for (String bioCondName : bioConditions) {
BioCondition bioCond = BioCondition.getBioCondition(bioCondName);
for (Tiling tiling : bioCond.getTilings()) {
if (!tiling.isInfoRead()) {
tiling.read();
omics.add(tiling);
}
}
for (OmicsData tscData : bioCond.getOmicsData()) {
if (tscData.getType() == TypeData.RNASeq) {
ExpressionData rnaseq = (ExpressionData) tscData;
rnaseq.load();
omics.add(rnaseq);
}
}
for (ProteomicsData proteome : bioCond.getProteomes()) {
if (!proteome.isLoaded()) {
proteome.load();
omics.add(proteome);
}
}
}
// Get expression of the gene in each omics dataset
for(OmicsData omic : omics) {
if(omic instanceof ExpressionData) {
if(omic.getType() == TypeData.RNASeq) {
ExpressionData ngs = (ExpressionData) omic;
double[] values = ngs.read(gene.getBegin(), gene.getEnd());
double value = VectorUtils.mean(values);
System.out.println("RNA expression of " +gene.getName() + " = "+ ngs.getName()+ " " + value);
}else if(omic.getType() == TypeData.Tiling) {
Tiling tiling = (Tiling) omic;
double[] values = tiling.get(gene.getBegin(), gene.getEnd(), true);
double value = VectorUtils.mean(values);
System.out.println("Tiling expression of " +gene.getName() + " = "+ tiling.getName()+ " " + value);
}
}else if(omic instanceof ProteomicsData) {
ProteomicsData proteome = (ProteomicsData) omic;
double value = proteome.getValue(gene.getName(), ""+ColNames.VALUE);
System.out.println("Proteome expression of " +gene.getName() + " = " + proteome.getName()+ " " + value);
}
}
Expected output with ListeriomicsSample
RNA expression of lmo0196 = BHI_2014_EGDe_f 8.947220907622064
RNA expression of lmo0196 = BHI_2014_EGDe_r 0.0
Tiling expression of lmo0196 = EGDe_280212.+.gr 7.040657774895381
Tiling expression of lmo0196 = EGDe_280212.-.gr 1.9403730330008202
Proteome expression of lmo0196 = Extracellular_BHI_2011_EGDe 2.0
Get transcriptome and proteome and correlate their expression value
String genomeName = Genome.EGDE_NAME;
Genome genome = Genome.loadGenome(genomeName);
//Select some datasets
ArrayList<String> bioConditions = new ArrayList<>();
bioConditions.add("BHI_2014_EGDe"); // RNASeq data
bioConditions.add("EGDe_280212"); // Tiling array data
bioConditions.add("Extracellular_BHI_2011_EGDe"); // proteomics data
/*
* Load all datasets (Load absolute expression values)
* Modified from: bacnet.genomeBrowser.core.DataTrack.loadData()
*/
ArrayList<OmicsData> omics = new ArrayList<OmicsData>();
for (String bioCondName : bioConditions) {
BioCondition bioCond = BioCondition.getBioCondition(bioCondName);
for (Tiling tiling : bioCond.getTilings()) {
if (!tiling.isInfoRead()) {
tiling.read();
omics.add(tiling);
}
}
for (OmicsData tscData : bioCond.getOmicsData()) {
if (tscData.getType() == TypeData.RNASeq) {
ExpressionData rnaseq = (ExpressionData) tscData;
rnaseq.load();
omics.add(rnaseq);
}
}
for (ProteomicsData proteome : bioCond.getProteomes()) {
if (!proteome.isLoaded()) {
proteome.load();
omics.add(proteome);
}
}
}
// Get expression of the genes in each omics dataset
HashMap<String, double[]> dataTOvalue = new HashMap<String, double[]>();
for(OmicsData omic : omics) {
System.out.println("Get expression value from "+omic.getName());
double[] valueOmic = new double[genome.getGeneNames().size()];
int k = 0;
for(String geneName : genome.getGeneNames()) {
Gene gene = genome.getGeneFromName(geneName);
if(omic instanceof ExpressionData) {
if(omic.getType() == TypeData.RNASeq) {
ExpressionData ngs = (ExpressionData) omic;
double[] values = ngs.read(gene.getBegin(), gene.getEnd());
double value = VectorUtils.mean(values);
valueOmic[k] = value;
}else if(omic.getType() == TypeData.Tiling) {
Tiling tiling = (Tiling) omic;
double[] values = tiling.get(gene.getBegin(), gene.getEnd(), true);
double value = VectorUtils.mean(values);
valueOmic[k] = value;
}
}else if(omic instanceof ProteomicsData) {
ProteomicsData proteome = (ProteomicsData) omic;
double value = proteome.getValue(gene.getName(), ""+ColNames.VALUE);
valueOmic[k] = value;
}
k++;
}
dataTOvalue.put(omic.getName(), valueOmic);
}
// calculate correlation
System.out.println(dataTOvalue.size());
for(int i=0;i<dataTOvalue.size();i++) {
String data1 = (String) dataTOvalue.keySet().toArray()[i];
for(int j=i+1;j<dataTOvalue.size();j++) {
String data2 = (String) dataTOvalue.keySet().toArray()[j];
double pearson = VectorUtils.pearsonCorrelation(dataTOvalue.get(data1), dataTOvalue.get(data2));
System.out.println("Pearson correlation " + data1 + " vs " + data2 + " = "+pearson);
}
}
Expected output with ListeriomicsSample
Get expression value from BHI_2014_EGDe_f
Get expression value from BHI_2014_EGDe_r
Get expression value from EGDe_280212.+.gr
Get expression value from EGDe_280212.-.gr
Get expression value from Extracellular_BHI_2011_EGDe
5
Pearson correlation BHI_2014_EGDe_r vs BHI_2014_EGDe_f = -0.41445242767486445
Pearson correlation BHI_2014_EGDe_r vs Extracellular_BHI_2011_EGDe = 0.18967716183382038
Pearson correlation BHI_2014_EGDe_r vs EGDe_280212.+.gr = -0.1271332697577054
Pearson correlation BHI_2014_EGDe_r vs EGDe_280212.-.gr = 0.8343485426119056
Pearson correlation BHI_2014_EGDe_f vs Extracellular_BHI_2011_EGDe = 0.09040552038115299
Pearson correlation BHI_2014_EGDe_f vs EGDe_280212.+.gr = 0.7916789004459144
Pearson correlation BHI_2014_EGDe_f vs EGDe_280212.-.gr = -0.24692357602934614
Pearson correlation Extracellular_BHI_2011_EGDe vs EGDe_280212.+.gr = 0.13169483731106035
Pearson correlation Extracellular_BHI_2011_EGDe vs EGDe_280212.-.gr = 0.15163077495892452
Pearson correlation EGDe_280212.+.gr vs EGDe_280212.-.gr = 0.04453016177144432
ExpressionMatrix matrix = ExpressionMatrix.loadTab("/Users/user/exprMatrix.txt", true);
matrix = Annotation.addAnnotation(matrix, Genome.loadEgdeGenome());
matrix.saveTab("/Users/user/exprMatrix_Annot.txt","Locustag");
This last piece of script has to be put in another function. It has be added to TestPart.runPostTests(EPartService partService). This is explained by the fact that GenomeViewer should be ran after the InitPage is created. All displays should be ran at the end of bacnet.e4.rap startup.
ArrayList<String> bioConditions = new ArrayList<>();
bioConditions.add("EGDe_280212");
bioConditions.add("BHI_2014_EGDe");
bioConditions.add("EGDe_37C_TSS");
bioConditions.add("EGDe_37C_RiboSeq");
bioConditions.add("EGDe_37C_TermSeq");
GenomeTranscriptomeView.displayGenomeElementAndBioConditions(partService, Genome.EGDE_NAME, bioConditions, "");
Expected output with ListeriomicsSample
-
First-Steps
-
Create ListeriomicsSample multi-omics website