Note: It is strongly recommended to create a virtual environment for each version of sci-loc2gene installed.
pip install scie2g
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 |