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setup.py
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111 lines (109 loc) · 7.65 KB
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#!/bin/env python
from setuptools import setup, find_packages
setup(
name="workScripts",
version="0.1",
python_requires='>=3.7.0',
description="Just some work scripts",
author="Julian Dosch",
author_email="Dosch@bio.uni-frankfurt.de",
url="https://github.com/JuRuDo/miscWorkscripts",
packages=find_packages(),
package_data={'': ['*']},
install_requires=[
'coreapi',
'urllib3',
'lxml',
'scanpy',
'matplotlib',
'celltypist',
'tifffile',
'plotly',
'pandas',
'openpyxl'
],
entry_points={
'console_scripts': ["uniprot.IDmapper = miscWorkScripts.uniprot.IDmapperUNIPROT:main",
"oma.getGroup = miscWorkScripts.oma.getGroup:main",
"kegg.getAAseq = miscWorkScripts.kegg.getAAseq:main",
"transcriptDEA.mergeResults = miscWorkScripts.transcriptDEA.mergeResults:main",
"transcriptDEA.fixEnsIDs = miscWorkScripts.transcriptDEA.fixEnsIDs:main",
"transcriptDEA.fixEnsIDsGeneExp = miscWorkScripts.transcriptDEA.fixEnsIDsGeneExp:main",
"transcriptDEA.getASevents = miscWorkScripts.transcriptDEA.compExpTranscripts:main",
"transcriptDEA.plotExp = miscWorkScripts.transcriptDEA.plotExp:main",
"transcriptDEA.plotExpCMS = miscWorkScripts.transcriptDEA.plotExpCMS:main",
"transcriptDEA.plotExpCMS2 = miscWorkScripts.transcriptDEA.plotExpCMS2:main",
"transcriptDEA.plotExp2 = miscWorkScripts.transcriptDEA.plotExp2:main",
"transcriptDEA.plotExpAS = miscWorkScripts.transcriptDEA.plotExpAS:main",
"transcriptDEA.plotExpAS2 = miscWorkScripts.transcriptDEA.plotExpAS2:main",
"transcriptDEA.plotExpAS3 = miscWorkScripts.transcriptDEA.plotExpAS3:main",
"transcriptDEA.getASgenes = miscWorkScripts.transcriptDEA.getASgenes:main",
"transcriptDEA.filterColumn = miscWorkScripts.transcriptDEA.getRowsById:main",
"transcriptDEA.createUniqueGeneIds = miscWorkScripts.transcriptDEA.unique_gene_id:main",
"transcriptDEA.cleanUnspecific = miscWorkScripts.transcriptDEA.removeUnspecificStrand:main",
"gsea.matchBGtoData = miscWorkScripts.gsea.matchBGtoData:main",
"gsea.bubblePlot = miscWorkScripts.gsea.bubblePlot:main",
"gsea.bubblePlotv2 = miscWorkScripts.gsea.bubblePlotv2:main",
"gsea.BToBbarplot = miscWorkScripts.gsea.BToBbarplot:main",
"dge.pca = miscWorkScripts.dge.pca:main",
"dge.pcaPlot = miscWorkScripts.dge.plotpca:main",
"dge.checkDGE = miscWorkScripts.dge.checkDGE:main",
"misc.filerTable = miscWorkScripts.misc.filterTable:main",
"misc.ENSGtoGeneName = miscWorkScripts.misc.ENSGtoGeneName:main",
"misc.matchTables = miscWorkScripts.misc.matchTables:main",
"misc.DGEcompareranks = miscWorkScripts.misc.DGEcompareranks:main",
"misc.plotTSNE = miscWorkScripts.misc.plotTSNE:main",
"misc.checkCountMatrix = miscWorkScripts.misc.checkCountMatrix:main",
"misc.plotBar = miscWorkScripts.misc.plotBar:main",
"misc.plotBox = miscWorkScripts.misc.plotBox:main",
"misc.mergeHtseq = miscWorkScripts.misc.mergeHtseq:main",
"misc.mergeStarGenecountOut = miscWorkScripts.misc.mergeStarGenecountOut:main",
"misc.plotHeatmap = miscWorkScripts.misc.plotHeatmap:main",
"misc.canonicalPercent = miscWorkScripts.misc.canonicalPercent:main",
"misc.plotSpatial = miscWorkScripts.misc.plotSpatial:main",
"misc.getProtLen = miscWorkScripts.misc.getProtLen:main",
"misc.plotBoxpanCK0 = miscWorkScripts.misc.plotBoxpanCK0:main",
"misc.readXML = miscWorkScripts.misc.readXML:main",
"misc.mapAffyxIDs = miscWorkScripts.misc.mapAffyxIDs:main",
"misc.mapGenomic = miscWorkScripts.misc.mapGenomic:main",
"misc.mapTranscriptomic = miscWorkScripts.misc.mapTranscriptomic:main",
"misc.mergeHtseqVar = miscWorkScripts.misc.mergeHtseqVar:main",
"misc.prepareHourglassData = miscWorkScripts.misc.prepareHourglassData:main",
"misc.tableToGMT = miscWorkScripts.misc.tableToGMT:main",
"misc.combineDisExp = miscWorkScripts.misc.combineDisExp:main",
"misc.plotGeneEnrichment = miscWorkScripts.misc.plotGeneEnrichment:main",
"misc.makeVenn = miscWorkScripts.misc.makeVenn:main",
"misc.transcriptTableFromGTF = miscWorkScripts.misc.transcriptTableFromGTF:main",
"misc.genesPerChromosome = miscWorkScripts.misc.genesPerChromosome:main",
"misc.plotChrDEstats = miscWorkScripts.misc.plotChrDEstats:main",
"misc.getRegionalDEgenes = miscWorkScripts.misc.getRegionalDEgenes:main",
"misc.filterFromFasta = miscWorkScripts.misc.filterFromFasta:main",
"misc.logRankTestByProtExp = miscWorkScripts.misc.logRankTestByProtExp:main",
"misc.protArrayRemDup = miscWorkScripts.misc.protArrayRemDup:main",
"misc.calcPearson = miscWorkScripts.misc.calcPearson:main",
"misc.readMutationsXLSX = miscWorkScripts.misc.readMutationsXLSX:main",
"misc.plotGSVAtoMutation = miscWorkScripts.misc.plotGSVAtoMutation:main",
"sce.makeHeatmap = miscWorkScripts.sce.make_heatmap:main",
"sce.plot_pca = miscWorkScripts.sce.plot_pca:main",
"sce.assignModules = miscWorkScripts.sce.assignModules:main",
"sce.processSCE = miscWorkScripts.sce.processSCE:main",
"sce.correlationPlot = miscWorkScripts.sce.correlationPlot:main",
"dge.plotVolcano = miscWorkScripts.dge.plotVolcano:main",
"spatial.XeniumToZarr = miscWorkScripts.spatial.XeniumToZarr:main",
"spatial.extractLevelXenium = miscWorkScripts.spatial.extractLevelXenium:main",
"spatial.combineDGEcsvs = miscWorkScripts.spatial.combineDGEcsvs:main",
"scanpy.01_setup_adata = miscWorkScripts.scanpy_scripts.S01_setup_adata:main",
"scanpy.02_process = miscWorkScripts.scanpy_scripts.S02_process:main",
"misc.merge_rTablecsv = miscWorkScripts.misc.merge_rTablecsv:main"
],
},
license="GPL-3.0",
classifiers=[
"Environment :: Console",
"Development Status :: 3 - Alpha",
"Intended Audience :: End Users/Desktop",
"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
"Natural Language :: English",
"Programming Language :: Python :: 3",
],
)