Tools for Batch Effects Diagnostics and Correction

adjust_batch_trend | adjust batch signal trend with the custom (continuous) fit |

color_list_to_df | Color list to data frame |

correct_batch | Correction of batch effects in the data |

correct_with_ComBat | Standardized input-output ComBat normalization ComBat allows... |

create_peptide_annotation | Prepare peptide annotation from long format data frame Create... |

dates_to_posix | Convert data/time to POSIXct |

date_to_sample_order | Convert date/time to POSIXct and rank samples by it |

example_peptide_annotation | Peptide annotation data |

example_proteome | Example protein data in long format |

example_proteome_matrix | Example protein data in matrix |

example_sample_annotation | Sample annotation data version 1 |

fit_nonlinear | Fit a non-linear trend |

generate_colors_for_numeric | Generates color list |

get_peptide_corr_df | Transform square correlation matrix into long data frame of... |

get_sample_corr_distrib | Calculates correlation distribution for all pairs of the... |

log_transform | Log transformation of the data, ensuring that the row and... |

long_to_matrix | Long to wide conversion |

matrix_to_long | Wide to long conversion |

merge_rare_levels | Replaces rare levels with other |

normalize | Data normalization methods |

normalize_data | Normalization brings the samples to the same scale |

normalize_sample_medians | Normalization by centering sample medians to global median of... |

plot_corr_matrix | Visualise correlation matrix |

plot_heatmap | Plot the heatmap of samples |

plot_hierarchical_clustering | cluster the data matrix to visually inspect which confounder... |

plot_iRT | Plot iRT measurements |

plot_PCA | plot PCA plot |

plot_peptide_corr_distribution | Plot distribution of peptide correlations within one protein... |

plot_peptides_of_one_protein | Plot peptides of one protein |

plot_protein_corrplot | Peptide correlation matrix (heatmap) |

plot_PVCA | Plot variance distribution by variable |

plot_sample_corr_distribution | Create violin plot of correlation distribution |

plot_sample_corr_heatmap | Sample correlation matrix (heatmap) |

plot_sample_mean_or_boxplot | Plot per-sample mean or boxplot (showing median and... |

plot_single_feature | Plot peptide measurements |

plot_spike_in | Plot spike-in measurements |

plot_with_fitting_curve | Plot peptide measurements across multi-step analysis |

proBatch | proBatch: A package for diagnostics and correction of batch... |

quantile_normalize | Quantile normalization of the data, ensuring that the row and... |

sample_annotation_to_colors | Generate colors for sample annotation |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.