Predicting Transcription Factor Binding Sites from ENCODE data using Machine Learning
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Updated
Jul 7, 2017 - Python
Predicting Transcription Factor Binding Sites from ENCODE data using Machine Learning
A pipeline for reporting information on G-quadruplexes relative to coding regions and non-aligned regions.
Tools for importing GFF files to a Neo4J graph database
home-made scripts to manipulate sequence annotation file formats (gff / vcf / genbank)
Modify the gff export from Apollo, changing Name to ID.
GTF parser for Java Dataframes
Convert sequence IDs between ucsc/refseq/genbank
Convert genome annotation GTF file into plain CSV format
Semantically Interoperable Genome Annotations
Evolutionary Bioinformatics Toolkit (EBT)
CRISPR/Cas-directed HDR genome editing suite: finds+scores gRNA targets, generates donor DNAs, & produces optimal cPCR primer designs.
The AgBioData GFF3 working group has developed recommendations to solve common problems in the GFF3 format. We suggest improvements for each of the GFF3 fields, as well as the special cases of modeling functional annotations, and standard protein-coding genes. We welcome discussion of these recommendations from the larger community.
scripts for RNA-Seq analysis
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