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[Tumor_Gene_Target_Screener]: Windows Fix #887

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merged 6 commits into from
Oct 20, 2023
Merged

[Tumor_Gene_Target_Screener]: Windows Fix #887

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d537ca3
[Tumor_Gene_Target_Screener]: Windows Fix
u8sand Jun 8, 2023
dfe1161
[Tumor_Gene_Target_Screener]: Add missing s3fs dependency
u8sand Jun 8, 2023
a0d7cda
[Tumor_Gene_Target_Screener]: Fix final table sort
u8sand Jun 20, 2023
f40733c
[Tumor_Gene_Target_Screener]: Adopt deterministic limma voom
u8sand Jun 20, 2023
ef715e0
[Tumor_Gene_Target_Screener]: Adopt newer maayanlab-bioinformatics patch
u8sand Jun 20, 2023
c4b0210
[Tumor_Gene_Target_Screener]: Freeze pandas version
u8sand Oct 20, 2023
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6 changes: 4 additions & 2 deletions appyters/Tumor_Gene_Target_Screener/Tumor_Gene_Target_Screener.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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\"<a href=\\\"https://cfde-gene-pages.cloud/gene/{g}\\\">{g}</a>\")\n",
"{% if membrane_screener %}\n",
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2 changes: 1 addition & 1 deletion appyters/Tumor_Gene_Target_Screener/appyter.json
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Expand Up @@ -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": [
{
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5 changes: 3 additions & 2 deletions appyters/Tumor_Gene_Target_Screener/requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
appyter
maayanlab-bioinformatics @ git+https://github.com/Maayanlab/[email protected].5
maayanlab-bioinformatics @ git+https://github.com/Maayanlab/[email protected].9
matplotlib
matplotlib_venn
numpy
pandas
pandas==2.0
plotly
qnorm
rpy2
s3fs
scikit-learn
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