Files in juanbot/CoExpNets
Co-expression network management based on WGCNA + k-means
.DS_Store
.Rbuildignore
.gitignore
CoExpNets.Rproj
DESCRIPTION
LICENSE
NAMESPACE
R/.gitignore
R/geneannot.R
R/main.R
R/naming.R
R/netdb.R
R/preservation.R
R/webapi.R
README.md
data/coexp.cell.categories.rda
data/coexp.cell.types.rda
data/coexp.cell.types.short.rda
data/coexp.external.cell.types.rda
data/coexp.external.cell.types.short.rda
data/coexp.friendly.cell.categories.rda
data/coexp.immune.cell.types.rda
data/coexp.long.friendly.cell.categories.ptp.rda
data/coexp.long.friendly.cell.categories.rda
data/coexp.neuronal.cell.types.rda
data/coexp.single.cell.types.rda
data/coexp.ukbec.cell.files.rda
data/coexp.ukbec.cell.types.rda
data/rosmap_small.rda
inst/EnsemblNamesGRCh38.txt
inst/GenCoExpNets.Rmd
inst/ICsBPhumanall.rda
inst/ICsCChumanall.rda
inst/ICsMFhumanall.rda
inst/IntroCoExp.Rmd
inst/Naming issues in CoExp.docx
inst/PrepExprData.Rmd
inst/TutorialIV.Rmd
inst/annot_19K.csv
inst/astrocytes20.txt
inst/astrocytes20.txt.txt
inst/cell_type_TableS1.csv
inst/cell_type_TableS1.csv.Astrocyte.txt
inst/cell_type_TableS1.csv.Bcells.txt
inst/cell_type_TableS1.csv.CA1.Pyramidal.txt
inst/cell_type_TableS1.csv.CA1_Pyramidal.txt
inst/cell_type_TableS1.csv.CD8Tcells.txt
inst/cell_type_TableS1.csv.Cytotoxiccells.txt
inst/cell_type_TableS1.csv.Dopaminergic.txt
inst/cell_type_TableS1.csv.DopaminergicNeuron.txt
inst/cell_type_TableS1.csv.Dopaminergic_Neuron.txt
inst/cell_type_TableS1.csv.Dopaminergic_Neuron_SN.txt
inst/cell_type_TableS1.csv.Dopaminergic_Neuron_VTA.txt
inst/cell_type_TableS1.csv.Endothelial.txt
inst/cell_type_TableS1.csv.Eosinophils.txt
inst/cell_type_TableS1.csv.Ependymal.txt
inst/cell_type_TableS1.csv.Ex1.txt
inst/cell_type_TableS1.csv.Ex2.txt
inst/cell_type_TableS1.csv.Ex3.txt
inst/cell_type_TableS1.csv.Ex4.txt
inst/cell_type_TableS1.csv.Ex5.txt
inst/cell_type_TableS1.csv.Ex6.txt
inst/cell_type_TableS1.csv.Ex7.txt
inst/cell_type_TableS1.csv.Ex8.txt
inst/cell_type_TableS1.csv.In1.txt
inst/cell_type_TableS1.csv.In2.txt
inst/cell_type_TableS1.csv.In3.txt
inst/cell_type_TableS1.csv.In4.txt
inst/cell_type_TableS1.csv.In5.txt
inst/cell_type_TableS1.csv.In6.txt
inst/cell_type_TableS1.csv.In7.txt
inst/cell_type_TableS1.csv.In8.txt
inst/cell_type_TableS1.csv.Interneuron.txt
inst/cell_type_TableS1.csv.Macrophages.txt
inst/cell_type_TableS1.csv.Mastcells.txt
inst/cell_type_TableS1.csv.Microglia.txt
inst/cell_type_TableS1.csv.Mural.txt
inst/cell_type_TableS1.csv.NaturalKillers.txt
inst/cell_type_TableS1.csv.Neuron.Ex1.txt
inst/cell_type_TableS1.csv.Neuron.Ex2.txt
inst/cell_type_TableS1.csv.Neuron.Ex3.txt
inst/cell_type_TableS1.csv.Neuron.Ex4.txt
inst/cell_type_TableS1.csv.Neuron.Ex5.txt
inst/cell_type_TableS1.csv.Neuron.Ex6.txt
inst/cell_type_TableS1.csv.Neuron.Ex7.txt
inst/cell_type_TableS1.csv.Neuron.Ex8.txt
inst/cell_type_TableS1.csv.Neuron.In1.txt
inst/cell_type_TableS1.csv.Neuron.In2.txt
inst/cell_type_TableS1.csv.Neuron.In3.txt
inst/cell_type_TableS1.csv.Neuron.In4.txt
inst/cell_type_TableS1.csv.Neuron.In5.txt
inst/cell_type_TableS1.csv.Neuron.In6.txt
inst/cell_type_TableS1.csv.Neuron.In7.txt
inst/cell_type_TableS1.csv.Neuron.In8.txt
inst/cell_type_TableS1.csv.Neuron_Dopaminergic.txt
inst/cell_type_TableS1.csv.Neuron_Dopaminergic_SNigra.txt
inst/cell_type_TableS1.csv.Neuron_Dopaminergic_VTA.txt
inst/cell_type_TableS1.csv.Neuron_Interneuron.txt
inst/cell_type_TableS1.csv.Neuron_Interneuton.txt
inst/cell_type_TableS1.csv.Neuron_Pyramidal_CA1.txt
inst/cell_type_TableS1.csv.Neuron_Pyramidal_S1.txt
inst/cell_type_TableS1.csv.Neutrophils.txt
inst/cell_type_TableS1.csv.Oligodendrocyte.txt
inst/cell_type_TableS1.csv.Pyramidal_CA1.txt
inst/cell_type_TableS1.csv.Pyramidal_S1.txt
inst/cell_type_TableS1.csv.S1.Pyramidal.txt
inst/cell_type_TableS1.csv.S1_Pyramidal.txt
inst/cell_type_TableS1.csv.SN_Dopaminergic.txt
inst/cell_type_TableS1.csv.SN_DopaminergicNeuron.txt
inst/cell_type_TableS1.csv.Tcells.txt
inst/cell_type_TableS1.csv.Tcm.txt
inst/cell_type_TableS1.csv.Tem.txt
inst/cell_type_TableS1.csv.Tfh.txt
inst/cell_type_TableS1.csv.Th1cells.txt
inst/cell_type_TableS1.csv.Th2cells.txt
inst/cell_type_TableS1.csv.Thelpercells.txt
inst/cell_type_TableS1.csv.VTA_Dopaminergic.txt
inst/cell_type_TableS1.csv.VTA_DopaminergicNeuron.txt
inst/cell_type_TableS1.csv.iDC.txt
inst/cell_type_TableS1.csv.tmp.csv
inst/ctall/Astrocyte.txt
inst/ctall/Bcells.txt
inst/ctall/CA1.Pyramidal.txt
inst/ctall/CA1_Pyramidal.txt
inst/ctall/CD8Tcells.txt
inst/ctall/Cerebellum_Basket_Neuroexpresso.txt
inst/ctall/Cerebellum_Bergmann_Neuroexpresso.txt
inst/ctall/Cerebellum_Golgi_Neuroexpresso.txt
inst/ctall/Cerebellum_Granule_Neuroexpresso.txt
inst/ctall/Cerebellum_MicrogliaActivation_Neuroexpresso.txt
inst/ctall/Cerebellum_MicrogliaDeactivation_Neuroexpresso.txt
inst/ctall/Cerebellum_Microglia_Neuroexpresso.txt
inst/ctall/Cerebellum_Oligo_Neuroexpresso.txt
inst/ctall/Cerebellum_Purkinje_Neuroexpresso.txt
inst/ctall/Cortex_Astrocyte_Neuroexpresso.txt
inst/ctall/Cortex_Endothelial_Neuroexpresso.txt
inst/ctall/Cortex_GabaPV_Neuroexpresso.txt
inst/ctall/Cortex_GabaRelnCalb_Neuroexpresso.txt
inst/ctall/Cortex_GabaVIPReln_Neuroexpresso.txt
inst/ctall/Cortex_MicrogliaActivation_Neuroexpresso.txt
inst/ctall/Cortex_MicrogliaDeactivation_Neuroexpresso.txt
inst/ctall/Cortex_Microglia_Neuroexpresso.txt
inst/ctall/Cortex_OligoPrecursors_Neuroexpresso.txt
inst/ctall/Cortex_Oligo_Neuroexpresso.txt
inst/ctall/Cortex_Pyramidal_Neuroexpresso.txt
inst/ctall/Cytotoxiccells.txt
inst/ctall/DAMANIS_MICROGLIA.txt
inst/ctall/DARMANIS_ASTROCYES.txt
inst/ctall/DARMANIS_ENDOTHELIAL.txt
inst/ctall/DARMANIS_FETAL1.txt
inst/ctall/DARMANIS_FETAL2.txt
inst/ctall/DARMANIS_MIXTURENEUASTRO.txt
inst/ctall/DARMANIS_MIXTURENEUOLIGOPC.txt
inst/ctall/DARMANIS_NEUROND.txt
inst/ctall/DARMANIS_OLIGO.txt
inst/ctall/DARMANIS_OPCS.txt
inst/ctall/D_NEuronCom1.txt
inst/ctall/D_NEuronCom2.txt
inst/ctall/D_NEuronCom3.txt
inst/ctall/D_NEuronCom4.txt
inst/ctall/D_NEuronCom5.txt
inst/ctall/D_NEuronCom6.txt
inst/ctall/D_NEuronCom7.txt
inst/ctall/Dopaminergic.txt
inst/ctall/DopaminergicNeuron.txt
inst/ctall/Dopaminergic_Neuron.txt
inst/ctall/Dopaminergic_Neuron_SN.txt
inst/ctall/Dopaminergic_Neuron_VTA.txt
inst/ctall/Endothelial.txt
inst/ctall/Eosinophils.txt
inst/ctall/Ependymal.txt
inst/ctall/Ex1.txt
inst/ctall/Ex2.txt
inst/ctall/Ex3.txt
inst/ctall/Ex4.txt
inst/ctall/Ex5.txt
inst/ctall/Ex6.txt
inst/ctall/Ex7.txt
inst/ctall/Ex8.txt
inst/ctall/GABASST_HIPPD_Neuroexpresso.txt
inst/ctall/Hippocampus_Astrocyte_Neuroexpresso.txt
inst/ctall/Hippocampus_DentateGranule_Neuroexpresso.txt
inst/ctall/Hippocampus_GabaSSTRein_Neuroexpresso.txt
inst/ctall/Hippocampus_MicrogliaActivation_Neuroexpresso.txt
inst/ctall/Hippocampus_MicrogliaDeactivation_Neuroexpresso.txt
inst/ctall/Hippocampus_Oligo_Neuroexpresso.txt
inst/ctall/Hippocampus_Pyramidal_Neuroexpresso.txt
inst/ctall/Hyppocampus_Microglia_Neuroexpresso.txt
inst/ctall/In1.txt
inst/ctall/In2.txt
inst/ctall/In3.txt
inst/ctall/In4.txt
inst/ctall/In5.txt
inst/ctall/In6.txt
inst/ctall/In7.txt
inst/ctall/In8.txt
inst/ctall/Interneuron.txt
inst/ctall/Macrophages.txt
inst/ctall/Mastcells.txt
inst/ctall/Microglia.txt
inst/ctall/Mural.txt
inst/ctall/NaturalKillers.txt
inst/ctall/Neuroexpress0_Cortex_Layer.2.3.Pyra.txt
inst/ctall/Neuroexpresso_CortexD_Endothelial.txt
inst/ctall/Neuroexpresso_CortexD_GabaPV.txt
inst/ctall/Neuroexpresso_CortexD_GabaRelnCalb.txt
inst/ctall/Neuroexpresso_CortexD_GabaVIPReln.txt
inst/ctall/Neuroexpresso_CortexD_Layer6bPyra.txt
inst/ctall/Neuroexpresso_CortexD_PyramidalCorticoThalam.txt
inst/ctall/Neuroexpresso_CortexD_Pyramidal_Glt_25d2.txt
inst/ctall/Neuroexpresso_CortexD_Pyramidal_S100a10.txt
inst/ctall/Neuroexpresso_Cortex_Laye.6aPyra.txt
inst/ctall/Neuroexpresso_Cortex_Layer4Pyra.txt
inst/ctall/Neuron.Ex1.txt
inst/ctall/Neuron.Ex2.txt
inst/ctall/Neuron.Ex3.txt
inst/ctall/Neuron.Ex4.txt
inst/ctall/Neuron.Ex5.txt
inst/ctall/Neuron.Ex6.txt
inst/ctall/Neuron.Ex7.txt
inst/ctall/Neuron.Ex8.txt
inst/ctall/Neuron.In1.txt
inst/ctall/Neuron.In2.txt
inst/ctall/Neuron.In3.txt
inst/ctall/Neuron.In4.txt
inst/ctall/Neuron.In5.txt
inst/ctall/Neuron.In6.txt
inst/ctall/Neuron.In7.txt
inst/ctall/Neuron.In8.txt
inst/ctall/Neuron_Dopaminergic.txt
inst/ctall/Neuron_Dopaminergic_SNigra.txt
inst/ctall/Neuron_Dopaminergic_VTA.txt
inst/ctall/Neuron_Interneuron.txt
inst/ctall/Neuron_Interneuton.txt
inst/ctall/Neuron_Pyramidal_CA1.txt
inst/ctall/Neuron_Pyramidal_S1.txt
inst/ctall/Neutrophils.txt
inst/ctall/Oligodendrocyte.txt
inst/ctall/PyramidalThy_HIPPD_Neuroexpresso.txt
inst/ctall/Pyramidal_CA1.txt
inst/ctall/Pyramidal_S1.txt
inst/ctall/S1.Pyramidal.txt
inst/ctall/S1_Pyramidal.txt
inst/ctall/SN_Dopaminergic.txt
inst/ctall/SN_DopaminergicNeuron.txt
inst/ctall/Tcells.txt
inst/ctall/Tcm.txt
inst/ctall/Tem.txt
inst/ctall/Tfh.txt
inst/ctall/Th1cells.txt
inst/ctall/Th2cells.txt
inst/ctall/Thelpercells.txt
inst/ctall/VTA_Dopaminergic.txt
inst/ctall/VTA_DopaminergicNeuron.txt
inst/ctall/iDC.txt
inst/dopaminergicneurons.txt
inst/dopaminergicneurons.txt.txt
inst/dopaminergicneurons_ens.txt
inst/loadgwasVEGASresults.txt
inst/loadgwasVEGASresults.txt.cogdnotxad.rosmap.fdrs.1
inst/loadgwasVEGASresults.txt.cogdnotxad.rosmap.fdrs.1.fet.csv
inst/loadgwasVEGASresults.txt.cogdnotxad.rosmap.fdrs.1.signals.csv
inst/loadgwasVEGASresults.txt.cogdxad.rosmap.fdrs.1
inst/loadgwasVEGASresults.txt.cogdxad.rosmap.fdrs.1.fet.csv
inst/loadgwasVEGASresults.txt.cogdxad.rosmap.fdrs.1.signals.csv
inst/mar/CellMarkersDarmanis2.csv
inst/mar/CellsMarkersDarmanis.csv
inst/mar/CellsMarkersDarmanis.xlsx
inst/mar/Cerebellum_Basket_Neuroexpresso.txt
inst/mar/Cerebellum_Bergmann_Neuroexpresso.txt
inst/mar/Cerebellum_Golgi_Neuroexpresso.txt
inst/mar/Cerebellum_Granule_Neuroexpresso.txt
inst/mar/Cerebellum_MicrogliaActivation_Neuroexpresso.txt
inst/mar/Cerebellum_MicrogliaDeactivation_Neuroexpresso.txt
inst/mar/Cerebellum_Microglia_Neuroexpresso.txt
inst/mar/Cerebellum_Oligo_Neuroexpresso.txt
inst/mar/Cerebellum_Purkinje_Neuroexpresso.txt
inst/mar/Cortex_Astrocyte_Neuroexpresso.txt
inst/mar/Cortex_Endothelial_Neuroexpresso.txt
inst/mar/Cortex_GabaPV_Neuroexpresso.txt
inst/mar/Cortex_GabaRelnCalb_Neuroexpresso.txt
inst/mar/Cortex_GabaVIPReln_Neuroexpresso.txt
inst/mar/Cortex_MicrogliaActivation_Neuroexpresso.txt
inst/mar/Cortex_MicrogliaDeactivation_Neuroexpresso.txt
inst/mar/Cortex_Microglia_Neuroexpresso.txt
inst/mar/Cortex_OligoPrecursors_Neuroexpresso.txt
inst/mar/Cortex_Oligo_Neuroexpresso.txt
inst/mar/Cortex_Pyramidal_Neuroexpresso.txt
inst/mar/DAMANIS_MICROGLIA.txt
inst/mar/DARMANIS_ASTROCYES.txt
inst/mar/DARMANIS_ENDOTHELIAL.txt
inst/mar/DARMANIS_FETAL1.txt
inst/mar/DARMANIS_FETAL2.txt
inst/mar/DARMANIS_MIXTURENEUASTRO.txt
inst/mar/DARMANIS_MIXTURENEUOLIGOPC.txt
inst/mar/DARMANIS_NEUROND.txt
inst/mar/DARMANIS_OLIGO.txt
inst/mar/DARMANIS_OPCS.txt
inst/mar/D_NEuronCom1.txt
inst/mar/D_NEuronCom2.txt
inst/mar/D_NEuronCom3.txt
inst/mar/D_NEuronCom4.txt
inst/mar/D_NEuronCom5.txt
inst/mar/D_NEuronCom6.txt
inst/mar/D_NEuronCom7.txt
inst/mar/GABASST_HIPPD_Neuroexpresso.txt
inst/mar/GenesCerebellumExpresso_toJuan.csv
inst/mar/GenesCerebellumExpresso_toJuan.xls
inst/mar/GenesCortex_NeuroExpresso_PYRAMIDALDEEPtoJuan.csv
inst/mar/GenesCortex_NeuroExpresso_PYRAMIDALDEEPtoJuan.xlsx
inst/mar/Hippocampus_Astrocyte_Neuroexpresso.txt
inst/mar/Hippocampus_DentateGranule_Neuroexpresso.txt
inst/mar/Hippocampus_GabaSSTRein_Neuroexpresso.txt
inst/mar/Hippocampus_MicrogliaActivation_Neuroexpresso.txt
inst/mar/Hippocampus_MicrogliaDeactivation_Neuroexpresso.txt
inst/mar/Hippocampus_Oligo_Neuroexpresso.txt
inst/mar/Hippocampus_Pyramidal_Neuroexpresso.txt
inst/mar/Hyppocampus_Microglia_Neuroexpresso.txt
inst/mar/ListGenesMarkersNeuroexpressoHIP_Juan.csv
inst/mar/ListGenesMarkersNeuroexpressoHIP_Juan.xlsx
inst/mar/NEUROEXPRESSO_CELLMARKERS_CORTEX_CONVERTHUMAN_JUAN.csv
inst/mar/NEUROEXPRESSO_CELLMARKERS_CORTEX_CONVERTHUMAN_JUAN.xlsx
inst/mar/Neuroexpress0_Cortex_Layer.2.3.Pyra.txt
inst/mar/Neuroexpresso_CortexD_Endothelial.txt
inst/mar/Neuroexpresso_CortexD_GabaPV.txt
inst/mar/Neuroexpresso_CortexD_GabaRelnCalb.txt
inst/mar/Neuroexpresso_CortexD_GabaVIPReln.txt
inst/mar/Neuroexpresso_CortexD_Layer6bPyra.txt
inst/mar/Neuroexpresso_CortexD_PyramidalCorticoThalam.txt
inst/mar/Neuroexpresso_CortexD_Pyramidal_Glt_25d2.txt
inst/mar/Neuroexpresso_CortexD_Pyramidal_S100a10.txt
inst/mar/Neuroexpresso_Cortex_Laye.6aPyra.txt
inst/mar/Neuroexpresso_Cortex_Layer4Pyra.txt
inst/mar/Neuroexpresso_DeepHippocampus_juan.csv
inst/mar/Neuroexpresso_DeepHippocampus_juan.xlsx
inst/mar/PyramidalThy_HIPPD_Neuroexpresso.txt
inst/mar/enrichment_tmp.csv
inst/nbia.txt
inst/neurons20.txt
inst/neurons20.txt.txt
inst/oligodendrocytes20.txt
inst/oligodendrocytes20.txt.txt
inst/pd_genes.txt
inst/pdgwas2014VEGASresults.txt
inst/pdgwas2014VEGASresults.txt.cogdxad.rosmap.fdrs.1
inst/pdgwas2014VEGASresults.txt.cogdxad.rosmap.fdrs.1.fet.csv
inst/pdgwas2014VEGASresults.txt.cogdxad.rosmap.fdrs.1.signals.csv
inst/tutorials/GeneAnnotation.html
inst/tutorials/GeneAnnotation.md
inst/tutorials/MyRosMap.3_Eigengenes_clustering.pdf
inst/tutorials/MyRosMap.3_dendro_colors.pdf
inst/tutorials/MyRosMap.3_mod_size.pdf
inst/tutorials/MyRosMap.4_Eigengenes_clustering.pdf
inst/tutorials/MyRosMap.4_dendro_colors.pdf
inst/tutorials/MyRosMap.4_mod_size.pdf
inst/tutorials/Tutorial_1
inst/tutorials/Tutorial_1.md
inst/tutorials/Tutorial_2.md
inst/tutorials/Tutorial_3.md
inst/tutorials/betastudyMyRosMap.signed.pdf
inst/tutorials/betastudyMyRosMap.signed.pdf.csv
inst/tutorials/netMyRosMap.4.it.20.rds
inst/tutorials/netMyRosMap.4.it.20.rds.Eigengenes_clustering.pdf
inst/tutorials/netMyRosMap.4.it.20.rds.USER_terms.csv
inst/tutorials/netMyRosMap.4.it.20.rds.celltype.pdf
inst/tutorials/netMyRosMap.4.it.20.rds.mod_size.pdf
inst/tutorials/netMyRosMap.4.it.20.rds_cor_pca_partitions.rds
inst/tutorials/netMyRosMap.4.it.20.rds_gprof.csv
man/addNet.Rd
man/addNetworkToDDBB.Rd
man/applyKMeans.Rd
man/dropGreyModule.Rd
man/fromAny2Ensembl.Rd
man/fromAny2GeneName.Rd
man/fromEnsembl2GeneNameBM.Rd
man/fromEntrez2Ensembl.Rd
man/fromGeneName2Ensembl.Rd
man/fromGeneName2EnsemblBM.Rd
man/fromXtIDToGeneSymbols19K.Rd
man/genCrossTabPlot.Rd
man/generateBetaStudy.Rd
man/getAndPlotNetworkLong.Rd
man/getBootstrapNetwork.Rd
man/getBootstrapNetworkCl.Rd
man/getCellTypeFromTissue.Rd
man/getDownstreamNetwork.Rd
man/getGOFromTissue.Rd
man/getGOFromTissues.Rd
man/getMM.Rd
man/getNetworkCategories.Rd
man/getNetworkFromTissue.Rd
man/initDb.Rd
man/loadConvTable.Rd
man/milkNet.Rd
man/plotMDS.Rd
man/plotModSizes.Rd
man/preservationOneWay.Rd
man/princePlot.Rd
man/readTOM.Rd
man/removeTOM.Rd
man/reportOnGeneIDs.Rd
man/reportOnGeneIDsGlobal.Rd
man/saveTOM.Rd
man/testGeneSet.Rd
webapi.R
