Man pages for TedCCLeung/PhotoperiodMotif
What the Package Does (One Line, Title Case)

addLeadingZerosAdd leading zeros to a numerical vector and convert it to...
CISBP_familiesDataframe of families of motifs from the CIS-BP database.
CISBP_motifsetMotif set from the CIS-BP database.
cluster_table_to_listConvert a cluster table to a list of list object
concatenate_FASTAConcatenate a list of FASTA files
concatenate_gff3Concatenate a list of GFF3 files
denovo_motifset1Motif set formed from de novo motif analysis with WEEDER,...
df_TFfamily_colorsDataframe of motif families from the CIS-BP database.
enrich_motifs_fisherFunction to clean up .meme motif files. Remove duplicate...
enrich_result_summaryProcessing of results from fisherEnrichMotif in a directory
filter_genes_by_rDEIFunction to filter gene IDs (TAIR IDs) based on daily...
genes_to_promoter_BiostringFunction to filter gene IDs (TAIR IDs) based on daily...
get_promotersFunction to return Biostring object with input of gene models
hclust_motifsPerform hierarchical clustering of motifs
heatmap_from_FisherPlot results of Fisher Exact Test as heat maps
heatmap_motif_clusteringPlot the result of hierarchical clustering of motifs
heatmap_motif_to_CISBP_familyRetrieve the motifs from a motif heatmap
heatmap_TF_familyPerform hierarchical clustering of motifs
JASPAR_motifsetMotif set from the JASPAR Plants database.
make_TAIR10_TxDbFunction to generate a TxDb object from the GenomicFeatures...
motif_clean_upFunction to clean up .meme motif files. Remove duplicate...
motif_to_CISBP_familySearch which family the most motif belongs to in CISBP
motif_to_similar_CISBPFind similar motifs against the CIS-BP motif database
photoperiodic_clustersPhotoperiodic clusters
pipePipe operator
pivotDFinDirMerge all the tabular text files in a directory and perform...
plot_positional_biasPlot the result from analyze_positional_bias
positional_biasAnalyse positional bias of motifs in a set of DNA sequences
positional_bias_subfuncAnalyse positional bias of motifs in a set of DNA sequences
rDEI_summaryTAIR10 gene models from Arabidopsis_thaliana.TAIR10.47.gtf
read_Fisher_resultRetrieve results from Fisher's Exact Test
read_genesRead a .txt file line by line and return a character vector.
run_enrichFunction to perform motif enrichment from motif mapping...
run_heatmapFunction to plot motif enrichment results as heat maps
run_inputFunction to take in motifs and sequences as inputs
run_mappingFunction to perform motif mapping
run_masterFunction to perform motif enrichment pipeline from motifs and...
TAIR10_GrangeGrange object from Arabidopsis_thaliana.TAIR10.47.gtf
theme_PrismTheme for imitating Prism
TedCCLeung/PhotoperiodMotif documentation built on April 27, 2022, 9:01 p.m.