[2023-06-07]
MOCA BLUE
MOtif Characterization & Annotation from DEEP LEARNING feature enrichment
Welcome the the moca_blue suite! from Simon M. Zumkeller RStudio 2022.07.2 Build 576
This is a tool-box for the analyses of DNA motifs that have been derived from deep-learning model features extraction. moca_blue is currently in development.
Please find more detailed descriptions of the directories and their role within them, respectively.
This is a pipeline of consecutive operations that can be and will be availabe here.
INPUT DIRECTORY /0MOTIFS /ref_seq - HDF5.file [feature extraction files] - fastas |____________ - gffs | | - meta-data START DIRECTORY /mo_nom /mo_range | output - get motif patterns - get motif meta-data | - motif annotation | | - motif modification | |_____________________________________| | | /mo_clu MAPPING to reference (external) - analyze motifs | use e.g. "blamm - compare/cluster | (https://github.com/biointec/blamm) | cp occurences.txt [results] /mo_proj || | /mo_proj - filter for meaningful matches - interpret model predictions - gene annotation - module generation
mo_nom --------------------------
Extract motifs from MoDisco hdf5 files and assign nomenclature. Currently, there are three versions of the same script that can be used for the extraction of a given format of weight matrix.
rdf5_get_xxx_per_pattern.v1.0R.R
PFM - positional frequence matrix PWM - positional weight matrix (best for clustering/comparison) CWM - contribution weight matrix (best for mapping)
mo_range ------------------------
Motifs/ EPMs are not distributed at random in a genome. To optimize the search for motifs/EPMs in a genome or gene-space, these tools extract the positionally preferred ranges for each motif/EPM in a hdf5 file.
rdf5_get_seql_per_patternV2.R - Extract a list of seqlets and their positions from the hdf5 file
meta_motif_ranges_characteristics_TSS-TTS.1.1.R - Producee a table from the rdf5_get_seql_per_patternV2.R output that provides the gene-space statistics for each motif/seqlet in reference to transcription start and stop sites (TSS, TTS)
mo_clu --------------------------
Analyse and Edit motif-files stored in jaspar-format here. Results should be stored in the "out" directory.
mo_cluster_v2.0R - generates dendrograms/trees based on distancy-matrix for different models.
mo_old ---------------------------
Old and outdated scripts used for the moca_blue suite are stored here.
ref_seq -------------------------
Store genome data like fasta, gff and many more here for INPUT.