Man pages for Ni-Ar/niar
Nice Interactive Analysis with R
| align_DNA_fasta | Align an input fasta file with Muscle |
| check_fasta | Helper function to check a fasta file that is going to be... |
| check_file | Helper function to check a file that is going to be imported... |
| col_freq | Helper function to use as a tidyverse verb |
| col_JS_divergence | Helper function to calculate the Jensen-Shannon divergence |
| col_sub_abs | Helper function to calculate the sum of the absolute... |
| count_snps_in_bins | Get how many SNPs variation fall within each bin in the... |
| dds2counts | Convert a DESeq2 dds object into a tibble |
| df2bits | Calculate the information content expressed in bits of... |
| df2JSD | Calculate Jensen-Shannon divergence (JSD) between 2 set of... |
| df2mat | Turn a dataframe into a matrix |
| df2pfm | Turn a data.frame with sequences into a positional frequency... |
| df2ppm | Turn a data.frame with sequences into a positional... |
| df2pwm | Create a PWM from a dataframe with sequences |
| encode_onehot | Perform one-hot encoding of any character string |
| ensembl_id_2_entrez | Convenient converter from ensembl ID to entrez ID |
| ensembl_id_2_gene_name | Convenient converter from ensembl ID to gene name |
| fasta2df | Handy wrapper to import fasta files into a data.frame |
| fasta2pim | Align a fasta file with MUSCLE and calculate the percentage... |
| filter_dds | Filter lowly abundant genes with the possibility of doing a... |
| find_containing_bin | Return the bin location of a num given a range from start... |
| gene_name_2_ensembl_id | Convenient converter from gene name to ensembl ID |
| get_alphabet_palette | Given an alphabet name set a palette for the plots. |
| get_hPTM_FC | Calculate summary stats across all samples for each hPTM and... |
| get_mouse_tissue_devel_tbl | Wrapper function to import pre-processed vast-tool analysis... |
| gimme_expr_mat | Extract the gene expression counts from an vast-tools... |
| gimme_mart | Handy function to create a biomaRt R object based on the... |
| gimme_PSI_expr_corr | Calculate correlation of one AS event PSI vs many genes... |
| gimme_psi_mat | Extract the PSI from an inclusion table and return it as a... |
| grep_gene_expression | Grep the expression values of a gene from a vast-tools output... |
| grep_psi | Grep the PSI values of an as event from a vast-tools output... |
| gtf_attributes_as_cols | Helper function to convert the last column list of a GTF file... |
| gtf_attributes_as_list | Helper function to handle the last column of a GTF file. |
| guess_alphabet | Guess an alphabet type in a dataframe sequences. |
| guess_species | Given a vast-tools AS event ID, return the species name. |
| hallgrimskirkja_plot | Title |
| inclusion_tbl2bed | Create a bed file from events in a vast-tools inclusion table |
| longest_common_prefix | Find the longest common prefix between 2 random names. If no... |
| longest_most_abundant_common_suffix | Find longest and most abundant common suffix |
| multiply_csv | Multiply comma-separated numbers in a character vector by a... |
| permutate_seq | Create same length sequence permutations for each letter |
| permutationz | My local function to enumerate the Permutations of the... |
| plotALLU_hPTM | Make an alluvial plot with the histone PTMs ratio in each... |
| plot_best_corr_genes | Plot to check the top and bottom correlating genes of one AS... |
| plot_bits_logo | Plot sequence information content as bits. |
| plot_corr_dist | Nice plot to check the density distribution of the... |
| plot_corr_gene_expr_psi | Plot a gene expression vs an alternatively spliced event PSI... |
| plot_corr_heatmap | Plot a heatmap with all correlations (many vs many) between... |
| plot_hist_dPSI | Plot the dPSI as an histogram using ggplot2 |
| plot_JSD_logo | Calculate and plot the Jensen-Shannon divergence between 2... |
| plotMA_hPTM | Plot the histone PTMs fold changes as an MA plot. |
| plot_mouse_tissue_devel | Nice plot to check expression and PSI across ENCODE mouse... |
| plot_pwm_as_bars | Visualise a PWM as a stacked barplot |
| plot_pwm_as_hm | Visualise a positional weight matrix as a heatmap |
| plot_rmats_summary | Plot the number of AS events quantified with rMATS-turbo |
| plot_rudimentary_JSD_logo | Quick visualisation of the Jensen-Shannon divergence |
| plot_rudimentary_logo | Quick visualisation of a logo. Not a fancy plot, just useful... |
| plot_samples_PSI | Plot the PSI of all samples in a data.frame |
| print_seq_perm | Pretty print a sequences permutation data frame |
| read_bed | Import a bed file into R as a tibble |
| read_EpiProfile_histone_ratio | Import EpiProfile version2.1 output file 'histone_ratio.xls'... |
| read_gtf | Import a GTF as tibble |
| read_rmats | Read rMATS Output Files and Process Splicing Event Data |
| read_rmats_summary | Import the rMATS-turbo summary files. |
| read_vst_tbl | Wrapper for 'readr::read_delim' for a tab delimited table.... |
| Rename_EpiProfile_colnames | Auxiliary function to modify the EpiProfile columns names on... |
| renumber_logo_seq_breaks | Given a sequence of upper and lower cases creates the best... |
| res2df | Work in PROGRESS. Convert a general DESeq2 result object into... |
| save_counts | Save the counts of a DESeq2 object. |
| save_df_gsea_list | This function is still experimental as it should be broken... |
| show_dds_counts_freq | Helper function to check distribution of reads in DESeq2... |
| showme_PCA2D | Given a matrix show me the principal components and other... |
| slop_bed | Extend upstream or downstream the coordinates of a bed file |
| test_regexes | Handy wrapper to grep regexes on multiple vectors |
| tidy_hPTMs | Parse the information about histone PTMs from an EpiProfile... |
| tidy_vst_expr | Reshape a wide vast-tools expression table to a long format |
| tidy_vst_psi | Reshape a wide vast-tools inclusion table into a... |
