This repository contains python code for the optional parts of labs in my Computations in Genetic Engineering (BME808) course at Ryerson University.
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Updated
Mar 15, 2017 - Python
This repository contains python code for the optional parts of labs in my Computations in Genetic Engineering (BME808) course at Ryerson University.
A simple way to map gene names/accession numbers/UniProt IDs/etc to other denominations in a Pandas Dataframe
Retrieve and create a custom BLAST database by taxonomic search
A python module to read and plot Galaxy RNA-seq data
IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results
Rat Genome Database to BEL
A Bio2BEL package for converting the Mouse Genome Informatics Database (MGI) to BEL
A Bio2BEL package for the terminology from FlyBase (http://flybase.org/)
A Bio2BEL package for converting Entrez and HomoloGene to BEL
Hugo Gene Nomenclature Consortium (HGNC) to BEL
A tool combining python, local blast, and the Ensembl REST API to design primers to genomic locations or genes.
EnsemblX is a Python applet with a simple GUI to speed up and simplify the process of referencing barley gene annotations from Ensembl Plants and BARLEX. Automates importing and processing of data from spreadsheets.
HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
My implementation of algorithm for defining genes in target panel.
A Silver Standard Corpus of Human Phenotype-Gene Relations
Creating so called sequence logos for UTRs and introns of genes in the human genome
Public REST API (Endpoint for testing purposes) for Ensembl Gene Autocompetion Table
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