Facilitate the integration

access_reactome | Return data from reactome |

allComb | Logical vectors of meta data |

analyze | Analyze a sgcca object |

angle | Calculates the angle between to slopes |

aves | Method to simplify AVE |

biological_relationships | Performs the calculation of biological information |

boot_evaluate | Evaluates the boostrapping of RGCCA |

boots_corr | Bootstrapping to asses how probable is to have such... |

boot_sgcca | Bootstrap sgcca |

cca_rgcca | Calculate correlation and covariance between CCA dimensions |

check_design | Validate designs |

circle | A circle of radium 2 |

circleFun | Create a circle |

clean_unvariable | Remove unvariable features |

colors | Useful colors |

comb_prevalence | Look for prevalene in combinations of two |

comp | Analyze the data for the relationship in time |

compare | Compares two objects of class sgcca |

compare.correlations | Calculates the z-score of two correlations |

contingency_taxa | Compares the taxonomy of the otus |

convert.z.score | Z-score to p-value |

correct | Check that the network is fully connected |

cor_sign | Significative correlation |

cors_rgcca | Check the efficacy of RGCCA |

dist2d | Calculate the distance between a line and a point |

ensembl2symbol | Translate ensmbl to symbols |

epitheliumE | Function to read the epithelium signature |

fastercheck | Check if a vector is in the matrix |

filter_RNAseq | Filter expressions |

filter_values | Filter correlations |

getAVEs | Retrieve inner AVE |

improve.sgcca | Improve the information on sgcca classes |

integration | Integrate |

Integration-package | Integrates data |

intercorrelation | Intracorrelation |

kFolding | Indexes for K-folds |

loo_functions | Function to export a function |

looIndex | Indexes without one sample |

makeRects | Make a rectangle at those cells |

McKeonHomeogenity | Calculates McKeon Homeogenity |

meta_i_norm | Normalize 16S biopsies metadata |

meta_r_norm | Normalize the metadata of the RNA |

meta_s_norm | Normalize 16S stools metadata |

model_columns | Adapt data for a CCA |

model_RGCCA | Prepare data for CCA. |

m_sem | Summarize a model |

norm_expr_colnames | Change names of expression |

norm_otus | Normalize OTUS |

norm_RNAseq | Normalize RNAseq |

pathsPerMicro | Enrichment by microorganisms |

permanova_expr | Permanova |

permanova_otus | Permanova |

plotAVEs | Distribution of inner AVE |

plot_cor | Plot a correlation with ggplot |

plot_interesting | Plot PCA of interesting variables |

plot_samples | Plot samples |

plot_single_cor | Plot correlations |

plot_variables | Plot bullseye |

prevalence | Test prevalence |

prevalence_tab | Calculates the presence or absence of a microorganism |

probability_samples | Calculates the probability of obtaining these samples. |

pvalue | Calculates the p.value |

ratio | Ratio of prevalence |

readSGCCA | Read component |

relevant | List the correlations |

select_genes_int | Filter genes |

select_var | Select important variables |

selectVar | Select variable from bootstrapping |

sem | Standard error of the mean |

sign_cor | List the correlations |

size | Number of samples |

store_micro | Store result by microorganism |

subsetData | Subset a list |

subSymm | Subsitute in a symmetric matrix |

symm | Create symmetric matrix |

taxonomy | Clean and prepare the data from IMNGS |

tidyer | Clean the output of a sgcca object |

tol21rainbow | Rainbow colors |

trimVer | Trim version number of genes |

two.sided | Two sided test |

variables | Extract in a tidy way the information about the variables |

variables_weight | Plot density of the weight of components |

weight_design | Check a design for different weights |

weights | Select the wegiths and adds information for human RNAseq |

weights_bayes | Independence between genes and OTUs |

weights_correlation | Correlation weights |

weights_otus | Select the wegiths and adds information for taxa RNAseq |

wilks_rgcca | Check the efficacy of RGCCA |

write_cor | Translate symbols and store |

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