bkutlu

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

# 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
library("org.Hs.eg.db")
library("tidyverse")

bkutlu

bkutlu

### script to find the length of the largest peptide for all the genes
### example demo for Mus Musculus

## load the necessary packages
library(dplyr)
library(biomaRt)
library(org.Mm.eg.db)
library(Biostrings)

## connect to Biomart Ensembl database and select mmusculus dataset