Burak Kutlu bkutlu

## working_with_conda.sh
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

## merge_bioC_Hs_gene_db.R
# 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")

## Convert+xgmml+file+to+igraph+object.ipynb

      
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                bkutlu
                / Convert+xgmml+file+to+igraph+object.ipynb
            
            
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              July 16, 2018 16:26
            
          
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## findLongestPeptide.R
### 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
	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
	# 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")
	### 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