Fixed installation issue by adapting scripts to Python 3.9 and Biopython 1.79
Updated find_differential.py script to speed up the finding of differential regions by integrating bedtools
Fixed the installation error caused by outdated logomaker package dependency (https://pypi.org/project/logomaker/)
Fixed bugs in concatenating files and maggie_vcf_input.py
Fixed bugs that will not terminate parallele processes when computing motif scores
Official release of MAGGIE v1.0!
Add script to find differential regions based on two BED files
Add function to split the input variants given in VCF file based on genomic annotations in GFF3 file
Fix bugs for VCF input; add a script to generate and conduct analysis on simulated sequences; upload histone QTL files
Update modules to extract sequences from reference genomes; add modules to generate simulated sequences
Now allow VCF file as input besides FASTA files!
Add information showing in the outputs, including numbers of motif mutation, summary and distribution of motif score differences
Incorporate redundant motifs from JASPAR 2020 database; \
Show logo of the top motif of the merged list in HTML output; \
Upload allele-specific CTCF, strain-specific PU.1, and QTLs datasets; \
Update environment configuration; \
Add progress bar.
Update computation pipeline and algorithm. Now accept FASTA files as inputs