Installing sci-epi2gene

Note: It is strongly recommended to create a virtual environment for each version of sci-loc2gene installed.

pip install scie2g

sci-epi2gene reference data

For ease of use we provide reference files for mouse and human, however, we recommend following the examples section which shows how to build these.

wget https://github.com/ArianeMora/sciepi2gene/data/hsapiens_gene_ensembl-GRCh38.p13.csv
wget https://github.com/ArianeMora/sciepi2gene/data/mmusculus_gene_ensembl-GRCm38.p6.csv

Examples using scibiomart to build references:

Human

scibiomart --m ENSEMBL_MART_ENSEMBL --d hsapiens_gene_ensembl --a "ensembl_gene_id,external_gene_name,chromosome_name,start_position,end_position,strand" --o "humanSorted" --s t

Mouse

scibiomart --m ENSEMBL_MART_ENSEMBL --d mmusculus_gene_ensembl --a "ensembl_gene_id,external_gene_name,chromosome_name,start_position,end_position,strand" --o "mm10Sorted" --s t

Below are supported versions of sci-epi2gene:

sci-epi2gene Release	Version
1	1.0.0