Lee Bergstrand's repositories
BackBLAST_Reciprocal_BLAST
This repository contains a reciprocal BLAST program for filtering down BLAST results to best bidirectional hits. It also contains a toolkit for finding and visualizing BLAST hits for gene clusters within multiple bacterial genomes.
Genbank-Downloaders
A series of small Biopython scripts for downloading sequence data off NCBI's Genbank.
Jupyter-SQLAlchemy-Tutorial
Introductory interactive Jupyter tutorial providing details about ORMs in order to assist in the teaching of their use to computing science students.
Bioinformatics_scripts
Scripts UBC
atlas-wrapper
A wrapper to run ATLAS within a Docker container
CDHITtoFASTA
Extracts CD-Hit clusters which contain reference proteins and stores them in FASTA format.
lee-bergstrand-msc-thesis
Lee Bergstrand's MSc. Thesis
BLAST-Mapper
An iPython notebook containing code for plotting BLAST hit position across multiple genomes using the Bokeh plotting library.
FragGeneScanPlusPlus
Scalable high-throughput short-read open reading frame prediction
gc_size_select
Visualization of genomic sequencing size selection protocol's influence on per fragment GC content.
hello-world
Just another repository
homebrew-bio
:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
homebrew-FragGeneScanPlusPlus
Homebrew formula for FragGeneScanPlusPlus
homebrew-science
:microscope: Scientific formulae for the Homebrew package manager
Phylogenetic-Tree-Building
A tool kit for extracting 16S rRNA genes from genomes for the purpose of building phylogenetic trees.
Torrent_Variant_Caller
Mirror of Ion Torrent's Ion Semiconductor Sequencing Variant Calling Software
TRU_ACM_ICPC
Thompson River University ACM International Collegiate Programming Contest Practice
watson-image-classifier
Image classifier using IBM Watson
yolo-tests
yolo-tests