Files in jmw86069/platjam
Platform Jam, biological platform importers.

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/coverjam-recenter-nmatlist.R R/covhm-validate-params.R R/jam-curate-to-df.R R/jam-design2colors.R R/jam-design2layout.R R/jam-numeric-to-colorfn.R R/jam-quick-complement-color.R R/jam_rmd_tab_iterator.R R/platjam-coverhm.R R/platjam-curate-se.R R/platjam-handle-df-args.R R/platjam-import-lipotype.R R/platjam-import-mascot.R R/platjam-import-metabolomics-niehs.R R/platjam-import-nanostring-csv.R R/platjam-import-omics-data.R R/platjam-import-proteomics.R R/platjam-import-salmonquant.R R/platjam-import.R R/platjam-merge-proteomics-se.R R/platjam-nanostring-rlf.R R/platjam-nanostring.R R/platjam-neuro.R R/platjam-ngs.R R/platjam-ucsctemplates.R R/platjam-ucsctracks.R R/platjam-word-wrap.R README.md TODO.md

_pkgdown.yml

data/jam_divergent.rda

data/jam_linear.rda

docs/404.html

docs/Coverage_Heatmaps_Notes.html

docs/TODO.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/news/index.html

docs/nmatlist2heatmsaps_args.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/1_DataProcessed/1_Input/compounds_neg.txt

docs/reference/1_DataProcessed/1_Input/compounds_pos.txt

docs/reference/Rplot001.png

docs/reference/Rplot002.png

docs/reference/Rplot003.png

docs/reference/Rplot004.png

docs/reference/Rplot005.png

docs/reference/Rplot006.png

docs/reference/Rplot007.png

docs/reference/Rplot008.png

docs/reference/applyXlsxConditionalFormatByColumn.html

docs/reference/assign_numeric_colors.html

docs/reference/assign_track_defaults.html

docs/reference/cardinality.html

docs/reference/color_complement-1.png

docs/reference/color_complement-2.png

docs/reference/color_complement-3.png

docs/reference/color_complement.html

docs/reference/convert_PD_df_to_SE.html

docs/reference/convert_imputed_assays_to_na.html

docs/reference/coverage_matrix2nmat-1.png

docs/reference/coverage_matrix2nmat.html

docs/reference/curate_se_colData.html

docs/reference/curate_to_df_by_pattern-1.png

docs/reference/curate_to_df_by_pattern.html

docs/reference/deepTools_matrix2nmat.html

docs/reference/design2colors-1.png

docs/reference/design2colors-2.png

docs/reference/design2colors-3.png

docs/reference/design2colors-4.png

docs/reference/design2colors-5.png

docs/reference/design2colors-6.png

docs/reference/design2colors.html

docs/reference/design2layout.html

docs/reference/df_to_numcolors.html

docs/reference/frequency_matrix2nmat.html

docs/reference/get_nmat_ceiling.html

docs/reference/get_numeric_transform.html

docs/reference/get_salmon_meta.html

docs/reference/get_salmon_root.html

docs/reference/get_track_defaults.html

docs/reference/handle_df_args.html

docs/reference/import_lipotype_csv.html

docs/reference/import_metabolomics_niehs.html

docs/reference/import_nanostring_csv.html

docs/reference/import_nanostring_rcc.html

docs/reference/import_nanostring_rlf.html

docs/reference/import_proteomics_PD.html

docs/reference/import_proteomics_mascot.html

docs/reference/import_salmon_quant.html

docs/reference/index.html

docs/reference/make_coverage_heatmaps-1.png

docs/reference/make_coverage_heatmaps-2.png

docs/reference/make_coverage_heatmaps-3.png

docs/reference/make_coverage_heatmaps-4.png

docs/reference/make_coverage_heatmaps-5.png

docs/reference/make_coverage_heatmaps.html

docs/reference/make_ucsc_trackname.html

docs/reference/mean_hue.html

docs/reference/merge_proteomics_se.html

docs/reference/nmathm_row_order.html

docs/reference/nmatlist2heatmaps-1.png

docs/reference/nmatlist2heatmaps-2.png

docs/reference/nmatlist2heatmaps-3.png

docs/reference/nmatlist2heatmaps-4.png

docs/reference/nmatlist2heatmaps-5.png

docs/reference/nmatlist2heatmaps-6.png

docs/reference/nmatlist2heatmaps-7.png

docs/reference/nmatlist2heatmaps-8.png

docs/reference/nmatlist2heatmaps.html

docs/reference/parse_salmon_flenfile.html

docs/reference/parse_ucsc_gokey.html

docs/reference/print_color_list.html

docs/reference/process_metab_compounds_file.html

docs/reference/quick_complement_color-1.png

docs/reference/quick_complement_color-2.png

docs/reference/quick_complement_color.html

docs/reference/rowNormScale.html

docs/reference/run_contrasts_se.html

docs/reference/run_se_contrasts.html

docs/reference/save_salmon_qc_xlsx.html

docs/reference/set_xlsx_colwidths.html

docs/reference/set_xlsx_rowheights.html

docs/reference/validate_heatmap_params.html

docs/reference/zoom_nmat.html

docs/reference/zoom_nmatlist.html

docs/sitemap.xml

exec/Coverage_Heatmaps_07dec2022.Rmd exec/call_coverage_heatmaps_Rmd.R

exec/call_coverage_heatmaps_Rscript.sh

inst/data/h3k4me1_coverage.matrix

inst/data/salmonOut/aux_info/meta_info.json

inst/data/salmonOut/cmd_info.json

inst/data/salmonOut/lib_format_counts.json

inst/data/tss_coverage.matrix

man/applyXlsxConditionalFormatByColumn.Rd man/apply_word_wrap.Rd man/assign_numeric_colors.Rd man/assign_track_defaults.Rd man/cardinality.Rd man/color_complement.Rd man/convert_PD_df_to_SE.Rd man/convert_imputed_assays_to_na.Rd man/coverage_matrix2nmat.Rd man/curate_se_colData.Rd man/curate_to_df_by_pattern.Rd man/deepTools_matrix2nmat.Rd man/design2colors.Rd man/design2layout.Rd man/df_to_numcolors.Rd man/frequency_matrix2nmat.Rd man/get_nmat_ceiling.Rd man/get_numeric_transform.Rd man/get_salmon_meta.Rd man/get_salmon_root.Rd man/get_track_defaults.Rd man/handle_df_args.Rd man/import_lipotype_csv.Rd man/import_metabolomics_niehs.Rd man/import_nanostring_csv.Rd man/import_nanostring_rcc.Rd man/import_nanostring_rlf.Rd man/import_omics_data.Rd man/import_proteomics_PD.Rd man/import_proteomics_mascot.Rd man/import_salmon_quant.Rd man/make_ucsc_trackname.Rd man/mean_hue.Rd man/merge_proteomics_se.Rd man/nmat_summary.Rd man/nmathm_row_order.Rd man/nmatlist2heatmaps.Rd man/nmatlist_summary.Rd man/parse_salmon_flenfile.Rd man/parse_ucsc_gokey.Rd man/print_color_list.Rd man/process_metab_compounds_file.Rd man/quick_complement_color.Rd man/recenter_nmatlist.Rd man/restrand_nmatlist.Rd man/rmd_tab_iterator.Rd man/rowNormScale.Rd man/save_salmon_qc_xlsx.Rd man/summit_from_vector.Rd man/validate_heatmap_params.Rd man/zoom_nmat.Rd man/zoom_nmatlist.Rd nmatlist2heatmsaps_args.md

platjam.Rproj

tests/testthat.R tests/testthat/test-assign-numeric-colors.R tests/testthat/test-curate-to-df.R

jmw86069/platjam documentation built on Sept. 26, 2024, 3:31 p.m.

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jmw86069/platjam
Platform Jam, biological platform importers.

Files in jmw86069/platjam
Platform Jam, biological platform importers.

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jmw86069/platjam Platform Jam, biological platform importers.

Files in jmw86069/platjam Platform Jam, biological platform importers.

R Package Documentation

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jmw86069/platjam
Platform Jam, biological platform importers.

Files in jmw86069/platjam
Platform Jam, biological platform importers.