├── .Rprofile ├── .gitattributes ├── .github └── workflows │ └── docker-image.yml ├── .gitignore ├── Dockerfile ├── Dockerfile.local ├── FragPipe-Analyst.Rproj ├── LICENSE ├── R ├── customized.R ├── demo_functions.R ├── enrichment_functions.R ├── filter.R ├── functions.R ├── tests.R └── volcano_function.R ├── README.md ├── data ├── create_example_data.R ├── demo_data.RData ├── example_data.RData └── lfq_results.RData ├── docs └── README.md ├── global.R ├── google_analytics.html ├── renv.lock ├── renv ├── .gitignore ├── activate.R └── settings.dcf ├── reports ├── DIA-peptide_report.Rmd ├── DIA-site_report.Rmd ├── DIA_report.Rmd ├── LFQ-peptide_report.Rmd ├── LFQ_report.Rmd ├── TMT-peptide_report.Rmd ├── TMT-site_report.Rmd └── TMT_report.Rmd ├── server.R ├── shiny-server.conf ├── shiny-server.conf.prod ├── ui.R └── www ├── CV_plot.png ├── Info.Rmd ├── Info.html ├── Info.md ├── Info_cache ├── html │ ├── __packages │ ├── exp_design_b71c6ebe27cac9dec05c8ffe7432463e.RData │ ├── exp_design_b71c6ebe27cac9dec05c8ffe7432463e.rdb │ └── exp_design_b71c6ebe27cac9dec05c8ffe7432463e.rdx └── markdown_strict │ ├── __packages │ ├── exp_design_ba255ed02e26d1f4a5a14728288efd24.RData │ ├── exp_design_ba255ed02e26d1f4a5a14728288efd24.rdb │ └── exp_design_ba255ed02e26d1f4a5a14728288efd24.rdx ├── LFQ-Analyst_manual.pdf ├── LFQ-Analyst_report.pdf ├── LFQ_analyst.png ├── LFQ_analyst.svg ├── PCA_plot.png ├── Protein_number.png ├── Protein_overlap.png ├── correlation_plot.png ├── css └── custom.css ├── data ├── experimental_design_example.txt ├── experimental_design_example_feb19.txt ├── proteinGroups_example.txt └── proteinGroups_example_feb19.txt ├── google-analytics.js ├── google_analytics.js ├── heatmap.png ├── imputation.png ├── js └── google_analytics.js ├── mbpf_logo.jpg ├── mbpf_logo.png ├── missing_heatmap.png ├── missing_quant.png ├── monash_logo.png ├── pvalue_hist.png └── volcano_plot.png /.Rprofile: -------------------------------------------------------------------------------- 1 | source("renv/activate.R") 2 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/docker-image.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/.github/workflows/docker-image.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/.gitignore -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/Dockerfile -------------------------------------------------------------------------------- /Dockerfile.local: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/Dockerfile.local -------------------------------------------------------------------------------- /FragPipe-Analyst.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/FragPipe-Analyst.Rproj -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/LICENSE -------------------------------------------------------------------------------- /R/customized.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/R/customized.R -------------------------------------------------------------------------------- /R/demo_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/R/demo_functions.R -------------------------------------------------------------------------------- /R/enrichment_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/R/enrichment_functions.R -------------------------------------------------------------------------------- /R/filter.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/R/filter.R -------------------------------------------------------------------------------- /R/functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/R/functions.R -------------------------------------------------------------------------------- /R/tests.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/R/tests.R -------------------------------------------------------------------------------- /R/volcano_function.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/R/volcano_function.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/README.md -------------------------------------------------------------------------------- /data/create_example_data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/data/create_example_data.R -------------------------------------------------------------------------------- /data/demo_data.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/data/demo_data.RData -------------------------------------------------------------------------------- /data/example_data.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/data/example_data.RData -------------------------------------------------------------------------------- /data/lfq_results.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/data/lfq_results.RData -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/docs/README.md -------------------------------------------------------------------------------- /global.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/global.R -------------------------------------------------------------------------------- /google_analytics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/google_analytics.html -------------------------------------------------------------------------------- /renv.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/renv.lock -------------------------------------------------------------------------------- /renv/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/renv/.gitignore -------------------------------------------------------------------------------- /renv/activate.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/renv/activate.R -------------------------------------------------------------------------------- /renv/settings.dcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/renv/settings.dcf -------------------------------------------------------------------------------- /reports/DIA-peptide_report.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/reports/DIA-peptide_report.Rmd -------------------------------------------------------------------------------- /reports/DIA-site_report.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/reports/DIA-site_report.Rmd -------------------------------------------------------------------------------- /reports/DIA_report.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/reports/DIA_report.Rmd -------------------------------------------------------------------------------- /reports/LFQ-peptide_report.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/reports/LFQ-peptide_report.Rmd -------------------------------------------------------------------------------- /reports/LFQ_report.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/reports/LFQ_report.Rmd -------------------------------------------------------------------------------- /reports/TMT-peptide_report.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/reports/TMT-peptide_report.Rmd -------------------------------------------------------------------------------- /reports/TMT-site_report.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/reports/TMT-site_report.Rmd -------------------------------------------------------------------------------- /reports/TMT_report.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/reports/TMT_report.Rmd -------------------------------------------------------------------------------- /server.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/server.R -------------------------------------------------------------------------------- /shiny-server.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/shiny-server.conf -------------------------------------------------------------------------------- /shiny-server.conf.prod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/shiny-server.conf.prod -------------------------------------------------------------------------------- /ui.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/ui.R -------------------------------------------------------------------------------- /www/CV_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/CV_plot.png -------------------------------------------------------------------------------- /www/Info.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Info.Rmd -------------------------------------------------------------------------------- /www/Info.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Info.html -------------------------------------------------------------------------------- /www/Info.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Info.md -------------------------------------------------------------------------------- /www/Info_cache/html/__packages: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Info_cache/html/__packages -------------------------------------------------------------------------------- /www/Info_cache/html/exp_design_b71c6ebe27cac9dec05c8ffe7432463e.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Info_cache/html/exp_design_b71c6ebe27cac9dec05c8ffe7432463e.RData -------------------------------------------------------------------------------- /www/Info_cache/html/exp_design_b71c6ebe27cac9dec05c8ffe7432463e.rdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Info_cache/html/exp_design_b71c6ebe27cac9dec05c8ffe7432463e.rdb -------------------------------------------------------------------------------- /www/Info_cache/html/exp_design_b71c6ebe27cac9dec05c8ffe7432463e.rdx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Info_cache/html/exp_design_b71c6ebe27cac9dec05c8ffe7432463e.rdx -------------------------------------------------------------------------------- /www/Info_cache/markdown_strict/__packages: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Info_cache/markdown_strict/__packages -------------------------------------------------------------------------------- /www/Info_cache/markdown_strict/exp_design_ba255ed02e26d1f4a5a14728288efd24.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Info_cache/markdown_strict/exp_design_ba255ed02e26d1f4a5a14728288efd24.RData -------------------------------------------------------------------------------- /www/Info_cache/markdown_strict/exp_design_ba255ed02e26d1f4a5a14728288efd24.rdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Info_cache/markdown_strict/exp_design_ba255ed02e26d1f4a5a14728288efd24.rdb -------------------------------------------------------------------------------- /www/Info_cache/markdown_strict/exp_design_ba255ed02e26d1f4a5a14728288efd24.rdx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Info_cache/markdown_strict/exp_design_ba255ed02e26d1f4a5a14728288efd24.rdx -------------------------------------------------------------------------------- /www/LFQ-Analyst_manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/LFQ-Analyst_manual.pdf -------------------------------------------------------------------------------- /www/LFQ-Analyst_report.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/LFQ-Analyst_report.pdf -------------------------------------------------------------------------------- /www/LFQ_analyst.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/LFQ_analyst.png -------------------------------------------------------------------------------- /www/LFQ_analyst.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/LFQ_analyst.svg -------------------------------------------------------------------------------- /www/PCA_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/PCA_plot.png -------------------------------------------------------------------------------- /www/Protein_number.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Protein_number.png -------------------------------------------------------------------------------- /www/Protein_overlap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/Protein_overlap.png -------------------------------------------------------------------------------- /www/correlation_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/correlation_plot.png -------------------------------------------------------------------------------- /www/css/custom.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/css/custom.css -------------------------------------------------------------------------------- /www/data/experimental_design_example.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/data/experimental_design_example.txt -------------------------------------------------------------------------------- /www/data/experimental_design_example_feb19.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/data/experimental_design_example_feb19.txt -------------------------------------------------------------------------------- /www/data/proteinGroups_example.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/data/proteinGroups_example.txt -------------------------------------------------------------------------------- /www/data/proteinGroups_example_feb19.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/data/proteinGroups_example_feb19.txt -------------------------------------------------------------------------------- /www/google-analytics.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/google-analytics.js -------------------------------------------------------------------------------- /www/google_analytics.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/google_analytics.js -------------------------------------------------------------------------------- /www/heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/heatmap.png -------------------------------------------------------------------------------- /www/imputation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/imputation.png -------------------------------------------------------------------------------- /www/js/google_analytics.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/js/google_analytics.js -------------------------------------------------------------------------------- /www/mbpf_logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/mbpf_logo.jpg -------------------------------------------------------------------------------- /www/mbpf_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/mbpf_logo.png -------------------------------------------------------------------------------- /www/missing_heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/missing_heatmap.png -------------------------------------------------------------------------------- /www/missing_quant.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/missing_quant.png -------------------------------------------------------------------------------- /www/monash_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/monash_logo.png -------------------------------------------------------------------------------- /www/pvalue_hist.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/pvalue_hist.png -------------------------------------------------------------------------------- /www/volcano_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashProteomics/FragPipe-Analyst/HEAD/www/volcano_plot.png --------------------------------------------------------------------------------