Pinned Repositories
100-Days-Of-ML-Code
100 Days of ML Coding
2019-smORF
Scripts to identify small open reading frames using ribosome profiling data
af2complex
Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
bio-pipeline
My collection of light bioinformatics analysis pipelines for specific tasks
DupGen_finder
A pipeline used to identify different modes of duplicated gene pairs
FunGAP
FunGAP: fungal Genome Annotation Pipeline
Liftoff
An accurate GFF3/GTF lift over pipeline
qvina
Accurately speed up AutoDock Vina
ribotricer
A tool for accurately detecting actively translating ORFs from Ribo-seq data
scripts-for-SSR-project
128 Phytophthora Isolates Reveal Species-Specific Microsatellite Distribution
biogeeker's Repositories
biogeeker/hpcleap_dnds
Sliding window dN/dS vs. functional protein domain comparison tool. Given VectorBase gene id inputs it will aggregate various useful Bioinformatics information available, then allow the user to compare selective pressures acting along the protein sequence vs. an overlay of functional protein domain annotations.
biogeeker/ambigram
Evolutionary Chromosome Breakpoints Validator
biogeeker/Genome_annotation
These are scripts that I use frequently in genome annotation projects. Some of them have evolved awkwardly so the code is difficult to follw
biogeeker/mgra
biogeeker/selectionTools
Pipeline to take VCF through to Selection Analysis.
biogeeker/radar
Rapid Automatic Detection and Alignments of Repeats
biogeeker/scikit-ribo
Accurate estimation and robust modelling of translation dynamics at codon resolution
biogeeker/resnet-1k-layers
Deep Residual Networks with 1K Layers
biogeeker/uORFs
biogeeker/contig_merger
Perl script to merge assembled contigs that contain overlaps
biogeeker/RiboDiff
RiboDiff: Tool to detect changes in translational efficiency based on ribosome footprinting data
biogeeker/Ribosome-Binding-Site-Calculator-v1.0
The Ribosome Binding Site (RBS) Calculator can predict the translation initiation rate of a protein coding sequence in bacteria and design synthetic RBS sequences to rationally control the translation initiation rate. It is used to design synthetic biological systems.
biogeeker/Python-for-Genomic-Data-Science-2015-Coursera
Python for Genomic Data Science 2015 Coursera from Johns Hopkins University
biogeeker/vcfPytools
vcf file manipulation
biogeeker/Rosalind-1
Solutions to Rosalind Bioinformatics Problems
biogeeker/Bioinformatics-1