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bkutlu /
Last active January 8, 2020 00:42
Working with conda environments
conda create --name myenv
conda env update --file environment.yml
conda deactivate
conda remove --name myenv --all
# viewing the list of environments
conda env list
# intial set up of conda autoenvironments
bkutlu / merge_bioC_Hs_gene_db.R
Last active August 2, 2018 18:23
Prepare a table annotations for human genes using Bioconductor
# I am sure this can be done in a multiple of ways: but here's a nice example of use of Reduce for merging lists
# This particular use case if when you are trying to make a look up table for Human genes
# Check out Marc Carlson's Annotationdbi packages and tutorials for alternative ways (SQL) of retrieving the information
# Caution note:
# the unintended consequence of joining on the Entrez Gene ids is the Ensembl ids for alternative ids are lost and usually the
# alternative ensembl id is used
# load package from the BioConductor Project
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bkutlu / findLongestPeptide.R
Last active September 29, 2017 19:14
Finding the longest peptide lengths genome wide
### script to find the length of the largest peptide for all the genes
### example demo for Mus Musculus
## load the necessary packages
## connect to Biomart Ensembl database and select mmusculus dataset