diff --git a/appyters/Tumor_Gene_Target_Screener/Tumor_Gene_Target_Screener.ipynb b/appyters/Tumor_Gene_Target_Screener/Tumor_Gene_Target_Screener.ipynb index 22942f01..19ed016f 100644 --- a/appyters/Tumor_Gene_Target_Screener/Tumor_Gene_Target_Screener.ipynb +++ b/appyters/Tumor_Gene_Target_Screener/Tumor_Gene_Target_Screener.ipynb @@ -272,6 +272,7 @@ "outputs": [], "source": [ "%%appyter code_exec\n", + "import os\n", "import qnorm\n", "import numpy as np\n", "import pandas as pd\n", @@ -295,7 +296,7 @@ "import sys\n", "import contextlib\n", "@contextlib.contextmanager\n", - "def suppress_output(stdout=True, stderr=True, dest='/dev/null'):\n", + "def suppress_output(stdout=True, stderr=True, dest=os.devnull):\n", " ''' Usage:\n", " with suppress_output():\n", " print('hi')\n", @@ -697,6 +698,7 @@ "%%appyter code_eval\n", "\n", "with suppress_output():\n", + " df_bg_expr_norm.columns = df_bg_expr_norm.columns.to_flat_index().map(lambda s: ', '.join(s))\n", " dge = limma_voom_differential_expression(\n", " df_bg_expr_norm, df_expr_norm,\n", " voom_design=True,\n", @@ -845,7 +847,7 @@ "outputs": [], "source": [ "%%appyter code_exec\n", - "dge_final = dge[dge.score >= 1].sort_values(['score', 't'], ascending=False).iloc[:16]\n", + "dge_final = dge[dge.score >= 1].sort_values(['score', '-log(adj.P.Val)'], ascending=False).iloc[:16]\n", "pd.set_option('display.max_colwidth', None)\n", "dge_final['Link'] = dge_final['gene_symbol'].map(lambda g: f\"{g}\")\n", "{% if membrane_screener %}\n", diff --git a/appyters/Tumor_Gene_Target_Screener/appyter.json b/appyters/Tumor_Gene_Target_Screener/appyter.json index 7886d3be..c4f45a53 100644 --- a/appyters/Tumor_Gene_Target_Screener/appyter.json +++ b/appyters/Tumor_Gene_Target_Screener/appyter.json @@ -2,7 +2,7 @@ "$schema": "https://raw.githubusercontent.com/MaayanLab/appyter-catalog/main/schema/appyter-validator.json", "name": "Tumor_Gene_Target_Screener", "title": "Tumor Gene Target Screener", - "version": "0.3.7", + "version": "0.3.9", "description": "An appyter for gene target screening of tumors", "authors": [ { diff --git a/appyters/Tumor_Gene_Target_Screener/requirements.txt b/appyters/Tumor_Gene_Target_Screener/requirements.txt index 779bffb6..cbfae430 100644 --- a/appyters/Tumor_Gene_Target_Screener/requirements.txt +++ b/appyters/Tumor_Gene_Target_Screener/requirements.txt @@ -1,10 +1,11 @@ appyter -maayanlab-bioinformatics @ git+https://github.com/Maayanlab/maayanlab-bioinformatics@v0.5.5 +maayanlab-bioinformatics @ git+https://github.com/Maayanlab/maayanlab-bioinformatics@v0.5.9 matplotlib matplotlib_venn numpy -pandas +pandas==2.0 plotly qnorm rpy2 +s3fs scikit-learn \ No newline at end of file