diff --git a/README.md b/README.md index f5f45f6..a0266bf 100755 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ We provided the evaluation script using target function proposed in the manuscript, as well as a gene2vec file in word2vec format. ## Introduction -Gene2Vec is a distributed representation of genes based on co-expression. From a pure data-driven fashion, we trained a +Gene2Vec is a distributed representation of genes based on co-expression. From a pure data-driven fashion, we trained a 200-dimension vector representation of all human genes, using gene co-expression patterns in 984 data sets from the GEO databases. In this repository, we provided the relevent codes as well as pre-trained gene2vec files. @@ -25,6 +25,8 @@ cd Gene2vec/ pip install -r requirements.txt ``` +*NOTE: If you get an error with `certifi`, add `--ignore-installed certifi` to the end of the `pip install` command.* + ## Usage ### gene2vec.py diff --git a/requirements.txt b/requirements.txt index 73b85bd..4e1bd6f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,7 @@ tensorflow>=1.6.0 -gensim>=3.4.0 +gensim==3.4.0 numpy>=1.14.0 -matplotlib>=2.1.2 \ No newline at end of file +matplotlib>=2.1.2 +scikit-learn==0.18.2 +scipy==1.2.0 +MulticoreTSNE==0.1