addLeadingZeros | Add leading zeros to a numerical vector and convert it to... |
CISBP_families | Dataframe of families of motifs from the CIS-BP database. |
CISBP_motifset | Motif set from the CIS-BP database. |
cluster_table_to_list | Convert a cluster table to a list of list object |
concatenate_FASTA | Concatenate a list of FASTA files |
concatenate_gff3 | Concatenate a list of GFF3 files |
denovo_motifset1 | Motif set formed from de novo motif analysis with WEEDER,... |
df_TFfamily_colors | Dataframe of motif families from the CIS-BP database. |
enrich_motifs_fisher | Function to clean up .meme motif files. Remove duplicate... |
enrich_result_summary | Processing of results from fisherEnrichMotif in a directory |
filter_genes_by_rDEI | Function to filter gene IDs (TAIR IDs) based on daily... |
genes_to_promoter_Biostring | Function to filter gene IDs (TAIR IDs) based on daily... |
get_promoters | Function to return Biostring object with input of gene models |
hclust_motifs | Perform hierarchical clustering of motifs |
heatmap_from_Fisher | Plot results of Fisher Exact Test as heat maps |
heatmap_motif_clustering | Plot the result of hierarchical clustering of motifs |
heatmap_motif_to_CISBP_family | Retrieve the motifs from a motif heatmap |
heatmap_TF_family | Perform hierarchical clustering of motifs |
JASPAR_motifset | Motif set from the JASPAR Plants database. |
make_TAIR10_TxDb | Function to generate a TxDb object from the GenomicFeatures... |
motif_clean_up | Function to clean up .meme motif files. Remove duplicate... |
motif_to_CISBP_family | Search which family the most motif belongs to in CISBP |
motif_to_similar_CISBP | Find similar motifs against the CIS-BP motif database |
photoperiodic_clusters | Photoperiodic clusters |
pipe | Pipe operator |
pivotDFinDir | Merge all the tabular text files in a directory and perform... |
plot_positional_bias | Plot the result from analyze_positional_bias |
positional_bias | Analyse positional bias of motifs in a set of DNA sequences |
positional_bias_subfunc | Analyse positional bias of motifs in a set of DNA sequences |
rDEI_summary | TAIR10 gene models from Arabidopsis_thaliana.TAIR10.47.gtf |
read_Fisher_result | Retrieve results from Fisher's Exact Test |
read_genes | Read a .txt file line by line and return a character vector. |
run_enrich | Function to perform motif enrichment from motif mapping... |
run_heatmap | Function to plot motif enrichment results as heat maps |
run_input | Function to take in motifs and sequences as inputs |
run_mapping | Function to perform motif mapping |
run_master | Function to perform motif enrichment pipeline from motifs and... |
TAIR10_Grange | Grange object from Arabidopsis_thaliana.TAIR10.47.gtf |
theme_Prism | Theme for imitating Prism |
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