twesleyb/SwipProteomics
Analysis of Swip TMT Spatial Proteomics

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twesleyb/SwipProteomics: Analysis of Swip TMT Spatial Proteomics
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Files in twesleyb/SwipProteomics
Analysis of Swip TMT Spatial Proteomics

.Rbuildignore
.gitignore
ACKNOWLEDGEMENTS
DESCRIPTION
LICENSE
NAMESPACE
Py/__init__.py
Py/random_color.py
R/calcPartSim.R R/col2hex.R R/filtProt.R R/filtQC.R R/getContrast.R R/getVariance.R R/ggsavePDF.R R/ggsaveTable.R R/ggtheme.R R/imputeKNNpep.R R/lmTestContrast.R R/lmerTestContrast.R R/lmerTestProtein.R R/normIRS.R R/normSL.R R/normSP.R R/notin.R R/r.squaredGLMM.R R/rmOutlierPSM.R R/rmSmall.R R/scale01.R R/set_font.R R/summarize_prot.R R/tidyProt.R R/write_excel.R README.md analysis/1_WASH-iBioID/1_lmTest-BioID-analysis.R analysis/1_WASH-iBioID/2_Cytoscape-noa-edges.R analysis/2_SWIP-TMT/0_PD-data-preprocess.R analysis/2_SWIP-TMT/1_MSstatsTMT-analysis.R analysis/2_SWIP-TMT/2_Swip-TMT-normalization.R analysis/3_Clustering/1_generate-network.R
analysis/3_Clustering/2_leidenalg-clustering.py
analysis/3_Clustering/3_post-leidenalg.R analysis/3_Clustering/4_generate-PPI-network.R analysis/4_Module-Analysis/1_module-lmerTest-analysis.R analysis/4_Module-Analysis/2_module-GSEA.R analysis/5_Plotting/00_generate-colors.R analysis/5_Plotting/01_plot-proteins.R analysis/5_Plotting/02_plot-protein-profiles.R analysis/5_Plotting/03_plot-module-profiles.R analysis/5_Plotting/04_network-graph.R analysis/5_Plotting/05_Protein-PCA.R analysis/5_Plotting/06_plot-WASHC-profile.R analysis/5_Plotting/07_sample-PCA.R analysis/5_Plotting/08_generate-module-graphs.R analysis/5_Plotting/09_WASH-BioID-PCA.R analysis/5_Plotting/10_plot-variance.R
analysis/7_Shiny/module-profiles/rsconnect/shinyapps.io/twesleyb/module-profiles.dcf
analysis/README.md
data/BioID.zip
data/README.md
data/TMT.zip
data/alt_contrast.rda
data/alt_partition.rda
data/bioid_anno.rda
data/bioid_gene_map.rda
data/bioid_prot.rda
data/bioid_results.rda
data/bioid_se.rda
data/corum_prots.rda
data/cpm_partition.rda
data/endosome.rda
data/fibrinogen.rda
data/gene_lists.rda
data/gof_results.rda
data/impute_prot.rda
data/irs_prot.rda
data/leidenalg_partition.rda
data/lmerTest_results.rda
data/lopit_prots.rda
data/lysosome.rda
data/modularity_partition.rda
data/module_colors.rda
data/module_gof.rda
data/module_gsea.rda
data/module_results.rda
data/modules.rda
data/msstats_contrasts.rda
data/msstats_gene_map.rda
data/msstats_partition.rda
data/msstats_prot.rda
data/msstats_results.rda
data/msstats_sig_prots.rda
data/mut_color.rda
data/mut_vs_control.rda
data/norm_prot.rda
data/pd_annotation.rda
data/pd_psm.rda
data/poor_prots.rda
data/prot_varpart.rda
data/proteasome.rda
data/protein_gof.rda
data/psm_outliers.rda
data/rave.rda
data/samples.rda
data/select_paths.rda
data/sig_gsea.rda
data/sig_modules.rda
data/sig_prots.rda
data/sigmodules.rda
data/swip.rda
data/swip_colors.rda
data/swip_gene_map.rda
data/swip_module_gsea.rda
data/swip_module_results.rda
data/swip_partition.rda
data/swip_results.rda
data/swip_sig_prots.rda
data/swip_tmt.rda
data/uniprot_subcell.rda
data/wash_bioid.rda
data/wash_interactome.rda
data/washc_prots.rda
data/wt_color.rda
docs/SWIP-eLife-paper.pdf
elife-image.png
figures/pdf/main/Figure_01.pdf figures/pdf/main/Figure_02.pdf figures/pdf/main/Figure_03.pdf figures/pdf/main/Figure_04.pdf figures/pdf/main/Figure_05.pdf figures/pdf/main/Figure_06.pdf figures/pdf/main/Figure_07.pdf figures/pdf/main/Figure_08.pdf figures/pdf/main/Figure_09.pdf figures/pdf/main/main.pdf figures/pdf/supp/Figure 1_figure supplement_1.pdf figures/pdf/supp/Figure 2_figure supplement_1.pdf figures/pdf/supp/Figure 3_figure supplement_1.pdf figures/pdf/supp/Figure 3_figure supplement_2.pdf figures/pdf/supp/Figure 3_figure supplement_3.pdf figures/pdf/supp/Figure 3_figure supplement_4.pdf figures/pdf/supp/Figure 3_figure supplement_5.pdf figures/pdf/supp/Figure 4_figure supplement_1.pdf figures/pdf/supp/Figure 4_figure supplement_2.pdf figures/pdf/supp/Figure 6_figure supplement_1.pdf figures/pdf/supp/Figure 6_figure supplement_2.pdf figures/pdf/supp/Figure 7_figure supplement_1.pdf figures/pdf/supp/Figure 7_figure supplement_2.pdf figures/pdf/supp/Figure 8_figure supplement_1.pdf figures/pdf/supp/supplement.pdf
fonts/arial.ttf
man/calcPartSim.Rd man/col2hex.Rd man/filtQC.Rd man/getContrast.Rd man/getVariance.Rd man/ggsavePDF.Rd man/ggsaveTable.Rd man/ggtheme.Rd man/grapes-notin-grapes.Rd man/imputeKNNpep.Rd man/lmTestContrast.Rd man/lmerTestContrast.Rd man/lmerTestProtein.Rd man/logRatios.Rd man/normIRS.Rd man/rmOutlierPSM.Rd man/rmSmall.Rd man/scale01.Rd man/set_font.Rd man/sumProt.Rd man/tidyProt.Rd man/write_excel.Rd sequences/dna/README.md
sequences/dna/pAAV-hSYN1-Washc1-BioID2-HA.dna
sequences/dna/pAAV2-1.dna
sequences/dna/pAAV2-9.dna
sequences/dna/pAdDeltaF6.gbk
sequences/dna/pmCAG-SWIP_MUT-HA.dna
sequences/dna/pmCAG-SWIP_WT-HA.dna
sequences/protein/README.md
sequences/protein/Swip.gif
sequences/protein/Swip_1019PR.pse
sequences/protein/Swip_P1019R.pdb
sequences/protein/Swip_WT.pdb
sequences/protein/Swip_WT.pse
sequences/protein/hWASHC4.prot
sequences/protein/mWASHC4.prot
tables/S1_WASH-BioID-Results.xlsx
tables/S2_SWIP-TMT-Protein-Results.xlsx
tables/S3_SWIP-TMT-Module-Results.xlsx
tables/S4_SWIP-TMT-Module-GSEA.xlsx
twesleyb/SwipProteomics documentation built on Sept. 15, 2021, 7:38 a.m.

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