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D
DREBIOP_DR_Pathways-based
Commit 3f736ca9 authored by Belen Otero Carrasco's avatar Belen Otero Carrasco
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processed data

parent c77de110
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Showing with 26 additions and 26 deletions
Notebooks/Processed data/1.1 Target gene-based treated disease_CSBJ_DREBIOP.ipynb
View file @ 3f736ca9
...@@ -29,7 +29,7 @@ ...@@ -29,7 +29,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"cases_csbj = pd.read_csv(\"final_cases_csbj.tsv\", sep='\\t')\n", "cases_csbj = pd.read_csv(\"./Data/Input/DISNET/final_cases_csbj.tsv\", sep='\\t')\n",
"cases_csbj = cases_csbj.drop([\"Unnamed: 0\"],axis=1)" "cases_csbj = cases_csbj.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
...@@ -39,7 +39,7 @@ ...@@ -39,7 +39,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"triplets_csbj = pd.read_excel(\"triplets_chembl_disnet.xlsx\",engine='openpyxl')\n", "triplets_csbj = pd.read_excel(\"./Data/Input/DISNET/triplets_chembl_disnet.xlsx\",engine='openpyxl')\n",
"triplets_csbj =triplets_csbj.drop([\"Unnamed: 0\"],axis=1)" "triplets_csbj =triplets_csbj.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
...@@ -101,7 +101,7 @@ ...@@ -101,7 +101,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"dis_gen = pd.read_csv('dis_genes.tsv', sep='\\t')\n", "dis_gen = pd.read_csv('./Data/Input/DISNET/dis_genes.tsv', sep='\\t')\n",
"dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)" "dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
...@@ -120,7 +120,7 @@ ...@@ -120,7 +120,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"drug_gen = pd.read_csv('drug_gen.tsv', sep='\\t')\n", "drug_gen = pd.read_csv('./Data/Input/DISNET/drug_gen.tsv', sep='\\t')\n",
"drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)" "drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
...@@ -171,7 +171,7 @@ ...@@ -171,7 +171,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"dis_path_direct = pd.read_csv('disease_pathway.tsv', sep='\\t')" "dis_path_direct = pd.read_csv('./Data/Input/DISNET/disease_pathway.tsv', sep='\\t')"
] ]
}, },
{ {
...@@ -196,7 +196,7 @@ ...@@ -196,7 +196,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"dis_gen_pw = pd.read_csv('dis_gen_pw.tsv', sep='\\t')\n", "dis_gen_pw = pd.read_csv('./Data/Input/DISNET/dis_gen_pw.tsv', sep='\\t')\n",
"dis_gen_pw = dis_gen_pw.drop([\"Unnamed: 0\"],axis=1)" "dis_gen_pw = dis_gen_pw.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
......
Notebooks/Processed data/1.2 Target gene-based treated disease_REPODB_DREBIOP.ipynb
View file @ 3f736ca9
...@@ -29,7 +29,7 @@ ...@@ -29,7 +29,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"cases_repodb = pd.read_csv(\"final_cases_repodb.tsv\", sep='\\t')" "cases_repodb = pd.read_csv(\"./Data/Input/DISNET/final_cases_repodb.tsv\", sep='\\t')"
] ]
}, },
{ {
...@@ -47,7 +47,7 @@ ...@@ -47,7 +47,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"triplets_repodb = pd.read_csv('repodb_all_triples.tsv', sep='\\t')" "triplets_repodb = pd.read_csv('./Data/Input/DISNET/repodb_all_triples.tsv', sep='\\t')"
] ]
}, },
{ {
...@@ -144,7 +144,7 @@ ...@@ -144,7 +144,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"dis_gen = pd.read_csv('dis_genes.tsv', sep='\\t')\n", "dis_gen = pd.read_csv('./Data/Input/DISNET/dis_genes.tsv', sep='\\t')\n",
"dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)" "dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
...@@ -183,7 +183,7 @@ ...@@ -183,7 +183,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"drug_gen = pd.read_csv('drug_gen.tsv', sep='\\t')\n", "drug_gen = pd.read_csv('./Data/Input/DISNET/drug_gen.tsv', sep='\\t')\n",
"drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)" "drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
...@@ -339,7 +339,7 @@ ...@@ -339,7 +339,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"dis_path_direct = pd.read_csv('disease_pathway.tsv', sep='\\t')" "dis_path_direct = pd.read_csv('./Data/Input/DISNET/disease_pathway.tsv', sep='\\t')"
] ]
}, },
{ {
...@@ -483,7 +483,7 @@ ...@@ -483,7 +483,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"dis_gen_pw = pd.read_csv('dis_gen_pw.tsv', sep='\\t')\n", "dis_gen_pw = pd.read_csv('./Data/Input/DISNET/dis_gen_pw.tsv', sep='\\t')\n",
"dis_gen_pw = dis_gen_pw.drop([\"Unnamed: 0\"],axis=1)" "dis_gen_pw = dis_gen_pw.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
......
Notebooks/Processed data/2. Processed data DREGE.ipynb
View file @ 3f736ca9
...@@ -29,7 +29,7 @@ ...@@ -29,7 +29,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"duples_repodb = pd.read_csv(\"repoDB_all_disdru.tsv\", sep='\\t')" "duples_repodb = pd.read_csv(\"./Data/Input/Drug Repurposing/repoDB_all_disdru.tsv\", sep='\\t')"
] ]
}, },
{ {
...@@ -38,7 +38,7 @@ ...@@ -38,7 +38,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"duples_csbj = pd.read_csv(\"duplas_CSBJ.tsv\")" "duples_csbj = pd.read_csv(\"./Data/Input/Drug Repurposing/duplas_CSBJ.tsv\")"
] ]
}, },
{ {
...@@ -173,7 +173,7 @@ ...@@ -173,7 +173,7 @@
} }
], ],
"source": [ "source": [
"dis_path_direct = pd.read_csv('disease_pathway.tsv', sep='\\t')\n", "dis_path_direct = pd.read_csv('./Data/Input/DISNET/disease_pathway.tsv', sep='\\t')\n",
"dis_path_direct" "dis_path_direct"
] ]
}, },
...@@ -183,7 +183,7 @@ ...@@ -183,7 +183,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"drug_gen = pd.read_csv('drug_gen.tsv', sep='\\t')" "drug_gen = pd.read_csv('./Data/Input/DISNET/drug_gen.tsv', sep='\\t')"
] ]
}, },
{ {
...@@ -201,7 +201,7 @@ ...@@ -201,7 +201,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"dis_gen = pd.read_csv('dis_genes_gda.tsv', sep='\\t')" "dis_gen = pd.read_csv('./Data/Input/DISNET/dis_genes_gda.tsv', sep='\\t')"
] ]
}, },
{ {
...@@ -219,7 +219,7 @@ ...@@ -219,7 +219,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"dis_gen_sinfil = pd.read_csv('dis_genes.tsv', sep='\\t')" "dis_gen_sinfil = pd.read_csv('./Data/Input/DISNET/dis_genes.tsv', sep='\\t')"
] ]
}, },
{ {
......
Notebooks/Processed data/2.1 Target gene-based treated disease _CSBJ-DREGE.ipynb
View file @ 3f736ca9
...@@ -29,7 +29,7 @@ ...@@ -29,7 +29,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"cases_csbj_target = pd.read_csv(\"cases_csbj_target.tsv\", sep =\"\\t\")\n", "cases_csbj_target = pd.read_csv(\"./Data/Input/DISNET/cases_csbj_target.tsv\", sep =\"\\t\")\n",
"cases_csbj = cases_csbj_target.drop([\"Unnamed: 0\"],axis=1)" "cases_csbj = cases_csbj_target.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
...@@ -59,7 +59,7 @@ ...@@ -59,7 +59,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"triplets_csbj = pd.read_excel(\"triplets_chembl_disnet.xlsx\",engine='openpyxl')" "triplets_csbj = pd.read_excel(\"./Data/Input/DISNET/triplets_chembl_disnet.xlsx\",engine='openpyxl')"
] ]
}, },
{ {
...@@ -167,7 +167,7 @@ ...@@ -167,7 +167,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"dis_gen = pd.read_csv('dis_genes.tsv', sep='\\t')\n", "dis_gen = pd.read_csv('./Data/Input/DISNET/dis_genes.tsv', sep='\\t')\n",
"dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)" "dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
...@@ -186,7 +186,7 @@ ...@@ -186,7 +186,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"drug_gen = pd.read_csv('drug_gen.tsv', sep='\\t')\n", "drug_gen = pd.read_csv('./Data/Input/DISNET/drug_gen.tsv', sep='\\t')\n",
"drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)" "drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
......
Notebooks/Processed data/2.2 Target gene-based treated disease_REPODB-DREGE.ipynb
View file @ 3f736ca9
...@@ -29,7 +29,7 @@ ...@@ -29,7 +29,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"cases_repodb = pd.read_csv(\"cases_repodb_target.tsv\", sep='\\t')\n", "cases_repodb = pd.read_csv(\"./Data/Input/DISNET/cases_repodb_target.tsv\", sep='\\t')\n",
"cases_repodb = cases_repodb.drop([\"Unnamed: 0\"],axis=1)" "cases_repodb = cases_repodb.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
...@@ -59,7 +59,7 @@ ...@@ -59,7 +59,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"triplets_repodb = pd.read_csv('repodb_all_triples.tsv', sep='\\t')" "triplets_repodb = pd.read_csv('./Data/Input/DISNET/repodb_all_triples.tsv', sep='\\t')"
] ]
}, },
{ {
...@@ -236,7 +236,7 @@ ...@@ -236,7 +236,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"dis_gen = pd.read_csv('dis_genes.tsv', sep='\\t')\n", "dis_gen = pd.read_csv('./Data/Input/DISNET/dis_genes.tsv', sep='\\t')\n",
"dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)" "dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
...@@ -275,7 +275,7 @@ ...@@ -275,7 +275,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"drug_gen = pd.read_csv('drug_gen.tsv', sep='\\t')\n", "drug_gen = pd.read_csv('./Data/Input/DISNET/drug_gen.tsv', sep='\\t')\n",
"drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)" "drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)"
] ]
}, },
......
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