{ "_id": "6a153b8cacfb0bcc41d52c32", "Type": "Package", "Package": "HDXBoxeR", "Title": "Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data", "Version": "0.0.2", "Authors@R": "c(person(\"Maria K.\", \"Janowska\", role = c(\"aut\", \"cre\"), \nemail=\"mka.janowska@gmail.com\",\ncomment = c(ORCID = \"0000-0002-8232-461X\")),\nperson(\"Katherine\", \"Reiter\", role = \"ctb\"),\nperson(\"Pearl\", \"Magala\", role = \"ctb\"),\nperson(\"Miklos\", \"Guttman\", role = \"ctb\"),\nperson(\"Rachel E.\", \"Klevit\", role = \"ctb\"))", "Author": "Maria K. Janowska [aut, cre]\n(), Katherine Reiter\n[ctb], Pearl Magala [ctb], Miklos Guttman [ctb], Rachel E.\nKlevit [ctb]", "Maintainer": "Maria K. Janowska ", "Description": "A protocol that facilitates the processing and analysis of\nHydrogen-Deuterium Exchange Mass Spectrometry data using\np-value statistics and Critical Interval analysis. It provides\na pipeline for analyzing data from 'HDXExaminer' (Sierra\nAnalytics, Trajan Scientific), automating matching and\ncomparison of protein states through Welch's T-test and the\nCritical Interval statistical framework. Additionally, it\nsimplifies data export, generates 'PyMol' scripts, and ensures\ncalculations meet publication standards. 'HDXBoxeR' assists in\nvarious aspects of hydrogen-deuterium exchange data analysis,\nincluding reprocessing data, calculating parameters,\nidentifying significant peptides, generating plots, and\nfacilitating comparison between protein states. For details\ncheck papers by Hageman and Weis (2019)\n and Masson et al. (2019)\n. 'HDXBoxeR' citation: Janowska\net al. (2024) .", "License": "GPL (>= 2)", "VignetteBuilder": "knitr, rmarkdown", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://mkajano.r-universe.dev", "Date/Publication": "2024-08-14 06:12:11 UTC", "RemoteUrl": "https://github.com/mkajano/hdxboxer", "RemoteRef": "HEAD", "RemoteSha": "63fdd47db29cfc589237ff67350de3aea76ea540", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 06:11:53 UTC", "User": "root" }, "MD5sum": "367dc4559101c92bd80fa0e825c18856", "_user": "mkajano", "_type": "src", "_file": "HDXBoxeR_0.0.2.tar.gz", "_fileid": "6c65b5976352ddbc841ba469bceab1e393159bc455728eb6cd666041306aa72b", "_filesize": 2771525, "_sha256": "6c65b5976352ddbc841ba469bceab1e393159bc455728eb6cd666041306aa72b", "_created": "2026-05-26T06:11:53.000Z", "_published": "2026-05-26T06:19:56.399Z", "_distro": "noble", "_jobs": [ { "job": 77817658674, "time": 129, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7210104156" }, { "job": 77817658690, "time": 152, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7210109070" }, { "job": 77817658708, "time": 155, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7210167095" }, { "job": 77817658678, "time": 165, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7210163525" }, { "job": 77817293660, "time": 189, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7210075608" }, { "job": 77817658671, "time": 106, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7210099473" }, { "job": 77817658738, "time": 100, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7210098203" }, { "job": 77817658684, "time": 109, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7210099967" }, { "job": 77817658688, "time": 107, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7210099346" } ], "_buildurl": "https://github.com/r-universe/mkajano/actions/runs/26435490899", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/mkajano/hdxboxer", "_commit": { "id": "63fdd47db29cfc589237ff67350de3aea76ea540", "author": "Maria Janowska ", "committer": "Maria Janowska ", "message": "another fix of the timecourse plots\n", "time": 1723615931 }, "_maintainer": { "name": "Maria K. Janowska", "email": "mka.janowska@gmail.com", "login": "mkajano", "description": "", "uuid": 11892713, "orcid": "0000-0002-8232-461X" }, "_registered": true, "_dependencies": [ { "package": "dplyr", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "wrapr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "mkajano", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "mkajano", "count": 64, "uuid": 11892713 } ], "_userbio": { "uuid": 11892713, "type": "user", "name": "Maria Janowska" }, "_downloads": { "count": 147, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/HDXBoxeR" }, "_devurl": "https://github.com/mkajano/hdxboxer", "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HDXBoxeR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/mkajano/hdxboxer", "_realowner": "mkajano", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2024-04-10" }, { "version": "0.0.2", "date": "2024-08-26" } ], "_exports": [ "all_summary", "arg_df", "arg_UN_FD", "arguments_call1", "arguments_call2", "arguments_call3", "av_tc", "av_tp", "ave_timepoint", "average_timecourse", "backHX_calculations", "boxplot_tp", "CI_2pts", "CI_single", "CI_tc", "CI_tp", "color_ranges_Blue_Red_heat_map", "color_ranges_Spectral", "coverage_residue", "deuteration_woods_timecourse", "deuteration_woods_timepoints", "dif_ave", "dif_tp", "dif_tp_proc", "duplicate_sets", "extreme_input_gap", "extreme_input_undeut", "general_info", "getCoords1", "heat_map_tc", "heat_map_tp", "heat_map_tp_maxuptake", "heat_map_tp_maxuptake_proc", "heat_map_tp_proc", "lab_dif", "lab_dif_proc", "lab_vol", "legend_heat_map", "legend_heat_map_tc", "legend_heat_map_timecourse", "legend_heat_map_tp", "legend_heat_map_tp_proc", "legend_nm_bottom", "legend_raw_ave", "legend_raw_ave_proc", "legend_raw_ave_tc", "legend_sig_peptides", "legend_states_PerD_bottom", "legend_tc_bottom", "nb_exch_deut", "nm_states", "output_FD", "output_FD_proc", "output_prep", "output_tc", "output_tp", "output_UD", "output_UD_proc", "pallette_legend", "pallette_ll", "peptide_pv_tp", "peptide_pv_tp_proc", "pl_gen_ch2", "pl_gen_uptake", "plot_heat_map_max_uptake_tp", "plot_heat_map_max_uptake_tp_proc", "plot_heat_map_tc", "plot_heat_map_tp", "plot_heat_map_tp_proc", "plot_peptide_sig_tp", "plot_peptide_sig_tp_proc", "plots_av_tcourse", "plots_av_tp", "plots_av_tp_proc", "plots_diff_tp", "plots_diff_tp_proc", "plots_vol_tp", "ppar", "ppar_bottom_legend", "ppar_wider", "pparLM", "prep_timecourse_plot_ave", "prep_timecourse_plot_sd", "pv_timecourse", "pv_timepoint", "pymol_script_average_residue", "pymol_script_significant_peptide", "pymol_script_significant_peptide_proc", "pymol_script_significant_residue", "pymol_script_significant_residue_proc", "pymol_str", "qpcr.cbind.na", "ranges_function", "ranges_function_tc", "rbind_na", "reset_par", "robot_2states_indexes", "robot_indexes", "robot_indexes_df", "robot_plot_All", "sd_timecourse", "sd_timecourse_proc", "sd_timepoint", "select_indices", "significant_peptide_uptake", "summary_sd_CI", "uptake_plots", "verbose_timecourse_output", "verbose_timepoint_output", "vol_tp", "woods_CI_plot" ], "_help": [ { "page": "all_summary", "title": "Returns full summary table.", "topics": [ "all_summary" ] }, { "page": "arg_df", "title": "Returns initially processed data.frame from the export from the HDXExaminer", "topics": [ "arg_df" ] }, { "page": "arg_UN_FD", "title": "Returns initially processed data.frame from the export from the HDXExaminer", "topics": [ "arg_UN_FD" ] }, { "page": "arguments_call1", "title": "Returns default arguments for the output_tp functions. States", "topics": [ "arguments_call1" ] }, { "page": "arguments_call2", "title": "Returns default arguments for the output_tp functions. Deut.Time", "topics": [ "arguments_call2" ] }, { "page": "arguments_call3", "title": "Returns default arguments for the output_tp functions. # replicates", "topics": [ "arguments_call3" ] }, { "page": "av_tc", "title": "Preparatory function for average plot for timecourses", "topics": [ "av_tc" ] }, { "page": "av_tp", "title": "Preparatory function for average plot", "topics": [ "av_tp" ] }, { "page": "ave_timepoint", "title": "Returns average value for either uptake of procent data.", "topics": [ "ave_timepoint" ] }, { "page": "average_timecourse", "title": "Calculates average for time course data.", "topics": [ "average_timecourse" ] }, { "page": "backHX_calculations", "title": "Summary of backexchange summary", "topics": [ "backHX_calculations" ] }, { "page": "boxplot_tp", "title": "Plots boxplots for all the averages in the set", "topics": [ "boxplot_tp" ] }, { "page": "CI_2pts", "title": "Global confidence interval treshold from experimental standard deviation for 2 samples.", "topics": [ "CI_2pts" ] }, { "page": "CI_single", "title": "Global confidence interval treshold from experimental standard deviation for 1 sample", "topics": [ "CI_single" ] }, { "page": "CI_tc", "title": "Critial interval calculation two sets of timecourses", "topics": [ "CI_tc" ] }, { "page": "CI_tp", "title": "Global confidence interval treshold from experimental standard deviation", "topics": [ "CI_tp" ] }, { "page": "color_ranges_Blue_Red_heat_map", "title": "Returns color pallete from red to blue with number of colors for defined ranges", "topics": [ "color_ranges_Blue_Red_heat_map" ] }, { "page": "color_ranges_Spectral", "title": "Returns Spectral pallette with colors matching defined ranges", "topics": [ "color_ranges_Spectral" ] }, { "page": "coverage_residue", "title": "Returns coverage per residue", "topics": [ "coverage_residue" ] }, { "page": "deuteration_woods_timecourse", "title": "Return woods plots for the timecourse", "topics": [ "deuteration_woods_timecourse" ] }, { "page": "deuteration_woods_timepoints", "title": "Return woods plots for the timepoints", "topics": [ "deuteration_woods_timepoints" ] }, { "page": "dif_ave", "title": "Returns data frame with difference of averages between State1 and other states provided.", "topics": [ "dif_ave" ] }, { "page": "dif_tp", "title": "Preparatory function for difference plot", "topics": [ "dif_tp" ] }, { "page": "dif_tp_proc", "title": "Preparatory function for difference plot", "topics": [ "dif_tp_proc" ] }, { "page": "duplicate_sets", "title": "Duplicate set function", "topics": [ "duplicate_sets" ] }, { "page": "extreme_input_gap", "title": "Makes input for Extreme for bimodal analysis.", "topics": [ "extreme_input_gap" ] }, { "page": "extreme_input_undeut", "title": "Makes input for Extreme for bimodal analysis.", "topics": [ "extreme_input_undeut" ] }, { "page": "general_info", "title": "Provides summary table for all data.sets.", "topics": [ "general_info" ] }, { "page": "getCoords1", "title": "function from plotfunctions package", "topics": [ "getCoords1" ] }, { "page": "heat_map_tc", "title": "Plots heat maps for time courses.", "topics": [ "heat_map_tc" ] }, { "page": "heat_map_tp", "title": "Preparatory function for heat map", "topics": [ "heat_map_tp" ] }, { "page": "heat_map_tp_maxuptake", "title": "Preparatory function for heat map of maximum uptake per residue.", "topics": [ "heat_map_tp_maxuptake" ] }, { "page": "heat_map_tp_maxuptake_proc", "title": "Preparatory function for heat map of maximum procent deuteration per residue.", "topics": [ "heat_map_tp_maxuptake_proc" ] }, { "page": "heat_map_tp_proc", "title": "Preparatory function for heat map for procent deuteration", "topics": [ "heat_map_tp_proc" ] }, { "page": "is.nan.data.frame", "title": "Checks for NaN is data.frame", "topics": [ "is.nan.data.frame" ] }, { "page": "lab_dif", "title": "Legend for difference in averages plot.", "topics": [ "lab_dif" ] }, { "page": "lab_dif_proc", "title": "Preparatory function for difference plot for procent deuteration", "topics": [ "lab_dif_proc" ] }, { "page": "lab_vol", "title": "Preparatory function for volcano plot legends", "topics": [ "lab_vol" ] }, { "page": "legend_heat_map", "title": "Legend for the heatmaps prep function.", "topics": [ "legend_heat_map" ] }, { "page": "legend_heat_map_tc", "title": "Legend for the heatmaps for timecourses.", "topics": [ "legend_heat_map_tc" ] }, { "page": "legend_heat_map_timecourse", "title": "Legend for the heatmaps prep function for timecourses.", "topics": [ "legend_heat_map_timecourse" ] }, { "page": "legend_heat_map_tp", "title": "Legend for the heatmaps.Extracts names from data.frame", "topics": [ "legend_heat_map_tp" ] }, { "page": "legend_heat_map_tp_proc", "title": "Legend for the heatmaps percent.Extracts names from data.frame", "topics": [ "legend_heat_map_tp_proc" ] }, { "page": "legend_nm_bottom", "title": "Legend, bottom of the plots", "topics": [ "legend_nm_bottom" ] }, { "page": "legend_raw_ave", "title": "Legend for average plot.", "topics": [ "legend_raw_ave" ] }, { "page": "legend_raw_ave_proc", "title": "Preparatory function to draw legends for average procent", "topics": [ "legend_raw_ave_proc" ] }, { "page": "legend_raw_ave_tc", "title": "Legend for average deuteration plot for timecourse.", "topics": [ "legend_raw_ave_tc" ] }, { "page": "legend_sig_peptides", "title": "Legend for the significant peptides", "topics": [ "legend_sig_peptides" ] }, { "page": "legend_states_PerD_bottom", "title": "Legend, bottom of the plots", "topics": [ "legend_states_PerD_bottom" ] }, { "page": "legend_tc_bottom", "title": "Preparatory function returns legends for the timecourses.", "topics": [ "legend_tc_bottom" ] }, { "page": "nb_exch_deut", "title": "Number of exchangeable protons", "topics": [ "nb_exch_deut" ] }, { "page": "nm_states", "title": "Lists names of states in data sets", "topics": [ "nm_states" ] }, { "page": "output_FD", "title": "Prepares output for HDX-MS Full deuteration data", "topics": [ "output_FD" ] }, { "page": "output_FD_proc", "title": "Prepares output for HDX-MS Full deuteration data for procent deuteration.", "topics": [ "output_FD_proc" ] }, { "page": "output_prep", "title": "Prepares output with HDX-MS data for publications", "topics": [ "output_prep" ] }, { "page": "output_tc", "title": "Prepares output for HDX-MS for the deuteration uptake or percent deuteration for the time courses.", "topics": [ "output_tc" ] }, { "page": "output_tp", "title": "Prepares output for HDX-MS for the deuteration uptake or percent deuteration for the time points.", "topics": [ "output_tp" ] }, { "page": "output_UD", "title": "Prepares output for HDX-MS Undeuterated sample data.", "topics": [ "output_UD" ] }, { "page": "output_UD_proc", "title": "Prepares output for HDX-MS Undeuterated data for procent deuteration.", "topics": [ "output_UD_proc" ] }, { "page": "pallette_legend", "title": "Color scheme using heatmap. Legend Extracts names from data.frame", "topics": [ "pallette_legend" ] }, { "page": "pallette_ll", "title": "Color scheme using heatmap. Legend extracts names from data frame", "topics": [ "pallette_ll" ] }, { "page": "peptide_pv_tp", "title": "Preparatory function for significant peptide plots", "topics": [ "peptide_pv_tp" ] }, { "page": "peptide_pv_tp_proc", "title": "Preparatory function for showing peptides with significant differences between sets.", "topics": [ "peptide_pv_tp_proc" ] }, { "page": "pl_gen_ch2", "title": "Prepares the plot window for the woods functions", "topics": [ "pl_gen_ch2" ] }, { "page": "pl_gen_uptake", "title": "Prepares the plot window for the woods functions", "topics": [ "pl_gen_uptake" ] }, { "page": "plot_heat_map_max_uptake_tp", "title": "Plots heat maps for maximum uptake per residue.", "topics": [ "plot_heat_map_max_uptake_tp" ] }, { "page": "plot_heat_map_max_uptake_tp_proc", "title": "Plots heat maps for maximum procent deuteration per residue.", "topics": [ "plot_heat_map_max_uptake_tp_proc" ] }, { "page": "plot_heat_map_tc", "title": "Plots heat maps for time courses.", "topics": [ "plot_heat_map_tc" ] }, { "page": "plot_heat_map_tp", "title": "Plots heat maps for significant peptides.", "topics": [ "plot_heat_map_tp" ] }, { "page": "plot_heat_map_tp_proc", "title": "Plots heat maps for significant peptides.", "topics": [ "plot_heat_map_tp_proc" ] }, { "page": "plot_peptide_sig_tp", "title": "Significant peptide plots.", "topics": [ "plot_peptide_sig_tp" ] }, { "page": "plot_peptide_sig_tp_proc", "title": "Draws peptides with significant difefrences between sets.", "topics": [ "plot_peptide_sig_tp_proc" ] }, { "page": "plots_av_tcourse", "title": "Generates average deuteration plot for the time-course.", "topics": [ "plots_av_tcourse" ] }, { "page": "plots_av_tp", "title": "Returns average deuteration plot for timepoints in the data frame", "topics": [ "plots_av_tp" ] }, { "page": "plots_av_tp_proc", "title": "Returns average procent deuteration plot for time points", "topics": [ "plots_av_tp_proc" ] }, { "page": "plots_diff_tp", "title": "Returns difference in average plot for timepoints in the data frame", "topics": [ "plots_diff_tp" ] }, { "page": "plots_diff_tp_proc", "title": "Returns difference in average procent deuteration plot for timepoints in the data frame", "topics": [ "plots_diff_tp_proc" ] }, { "page": "plots_vol_tp", "title": "Returns volcano plots for timepoints in the data frame", "topics": [ "plots_vol_tp" ] }, { "page": "ppar", "title": "Preparation of figure window.", "topics": [ "ppar" ] }, { "page": "ppar_bottom_legend", "title": "Preparation of figure window with area for figure at the bottom.", "topics": [ "ppar_bottom_legend" ] }, { "page": "ppar_wider", "title": "Preparation of figure window with more area on west side of plot.", "topics": [ "ppar_wider" ] }, { "page": "pparLM", "title": "Preparation of figure window. small margins", "topics": [ "pparLM" ] }, { "page": "prep_timecourse_plot_ave", "title": "Prepares function for plotting averages in timecourse", "topics": [ "prep_timecourse_plot_ave" ] }, { "page": "prep_timecourse_plot_sd", "title": "Prepares function for Critical interval for timecourses", "topics": [ "prep_timecourse_plot_sd" ] }, { "page": "pv_timecourse", "title": "pvalue calculation between two sets of the data at certain timepoint", "topics": [ "pv_timecourse" ] }, { "page": "pv_timepoint", "title": "Calculation of pvalue between first protein state and any other state from all_states file", "topics": [ "pv_timepoint" ] }, { "page": "pymol_script_average_residue", "title": "Writes a text files with pymol scripts to list significant residues.", "topics": [ "pymol_script_average_residue" ] }, { "page": "pymol_script_significant_peptide", "title": "Writes a text files with pymol scripts to list significant peptides", "topics": [ "pymol_script_significant_peptide" ] }, { "page": "pymol_script_significant_peptide_proc", "title": "Writes a text files with pymol scripts to list significant peptides", "topics": [ "pymol_script_significant_peptide_proc" ] }, { "page": "pymol_script_significant_residue", "title": "Writes a text files with pymol scripts to list significant residues.", "topics": [ "pymol_script_significant_residue" ] }, { "page": "pymol_script_significant_residue_proc", "title": "Writes a text files with pymol scripts to list significant residues.", "topics": [ "pymol_script_significant_residue_proc" ] }, { "page": "pymol_str", "title": "Preparatory function writing pymol scripts", "topics": [ "pymol_str" ] }, { "page": "qpcr.cbind.na", "title": "Hidden function from qpcR package, typical usage as qpcR:::cbind.na", "topics": [ "qpcr.cbind.na" ] }, { "page": "ranges_function", "title": "Gives ranges for the averages", "topics": [ "ranges_function" ] }, { "page": "ranges_function_tc", "title": "Gives ranges for the averages for time course analysis", "topics": [ "ranges_function_tc" ] }, { "page": "rbind_na", "title": "bind non equal row", "topics": [ "rbind_na" ] }, { "page": "reset_par", "title": "Reset plotting window parameters to default", "topics": [ "reset_par" ] }, { "page": "robot_2states_indexes", "title": "Returns a robot plot for selected peptides for 2 protein states.", "topics": [ "robot_2states_indexes" ] }, { "page": "robot_indexes", "title": "Returns indexes for peptides with significant difference between two sets", "topics": [ "robot_indexes" ] }, { "page": "robot_indexes_df", "title": "Returns dataframe with peptides which exhibit significant difference between two sets", "topics": [ "robot_indexes_df" ] }, { "page": "robot_plot_All", "title": "Returns a robot plot for comparisons of the timepoints samples", "topics": [ "robot_plot_All" ] }, { "page": "sd_timecourse", "title": "Returns standard deviation for uptake data for timecourses.", "topics": [ "sd_timecourse" ] }, { "page": "sd_timecourse_proc", "title": "Returns standard deviation for percent deuteration data for timecourses.", "topics": [ "sd_timecourse_proc" ] }, { "page": "sd_timepoint", "title": "Returns standard deviation for dataframe.", "topics": [ "sd_timepoint" ] }, { "page": "select_indices", "title": "Allows for selecting some peptide from input data", "topics": [ "select_indices" ] }, { "page": "significant_peptide_uptake", "title": "Function returns which peptides are significantly based of pv_cutoff and Critial interval", "topics": [ "significant_peptide_uptake" ] }, { "page": "summary_sd_CI", "title": "Provides summary table with Critical interval and standard deviation within the set.", "topics": [ "summary_sd_CI" ] }, { "page": "uptake_plots", "title": "Uptake plots", "topics": [ "uptake_plots" ] }, { "page": "verbose_timecourse_output", "title": "Returns csv with averages from analysis for procent deuteration file, standard deviation for time courses.", "topics": [ "verbose_timecourse_output" ] }, { "page": "verbose_timepoint_output", "title": "Returns csv with averages from analysis for uptake file, standard deviation, p-values.", "topics": [ "verbose_timepoint_output" ] }, { "page": "vol_tp", "title": "Preparatory function for volcano plot", "topics": [ "vol_tp" ] }, { "page": "woods_CI_plot", "title": "Returns a woods plot for comparisons of the timepoints samples", "topics": [ "woods_CI_plot" ] } ], "_readme": "https://github.com/mkajano/hdxboxer/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "generics", "glue", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "rlang", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "wrapr" ], "_vignettes": [ { "source": "HDXBoxeR.Rmd", "filename": "HDXBoxeR.html", "title": "HDXBoxeR", "author": "Maria K. Janowska, Katherine Reiter, Pearl Magala, Miklos Guttman, Rachel E. Klevit", "engine": "knitr::rmarkdown", "headings": [ "How to use this vignette?", "1. Input preparation", "Input preparation", "2. Installation & Loading", "3. How to load data into R", "4. Statistical Analysis", "Some theoretical details about statistical analysis", "Practical Tips for Statistical Analysis in HDXBoxeR", "States, Replicates, Timepoints, etc.", "Sub-setting of the Input Table", "5. Plots", "Uptake Plots", "Boxplots", "Average uptake and procent deuteration plots per time-point", "Difference Uptake or Percent Deuteration Plots per Time-point", "Volcano Plots", "Significant Peptides Mapped Along Residue Sequence", "Differential heat maps", "Woods Plots", "Timecourse Plots", "Robot Plots", "Woods_CI plots", "6. Scripts for Pymol", "7. Summary Information Generation about Data Sets", "8. Outputs", "9. Preparation Inputs for Bimodal Analysis for HX-Express v2", "10. Proposed Workflow.", "11. List of all functions & parameters." ], "created": "2021-03-03 06:22:43", "modified": "2024-08-14 06:12:11", "commits": 19 } ], "_score": 4, "_indexed": true, "_nocasepkg": "hdxboxer", "_universes": [ "mkajano" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.2", "date": "2026-05-26T06:13:57.000Z", "distro": "noble", "commit": "63fdd47db29cfc589237ff67350de3aea76ea540", "fileid": "79d88b9328d8ee2948f20a3df5ffbd6b7d9bbc1ac6ba87e8bf7d8dccec6085b4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mkajano/actions/runs/26435490899" }, { "r": "4.6.0", "os": "linux", "version": "0.0.2", "date": "2026-05-26T06:14:16.000Z", "distro": "noble", "commit": "63fdd47db29cfc589237ff67350de3aea76ea540", "fileid": "9ba730a6e1e11fd501e537f35fed9fe79c8c48ad15bfcc08b965ffa96f3bd7c7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mkajano/actions/runs/26435490899" }, { "r": "4.5.3", "os": "mac", "version": "0.0.2", "date": "2026-05-26T06:18:58.000Z", "commit": "63fdd47db29cfc589237ff67350de3aea76ea540", "fileid": "d7111f28cdd09450bf9c3a92b0921908c4061131abc44db292827d3c71acd0d8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mkajano/actions/runs/26435490899" }, { "r": "4.6.0", "os": "mac", "version": "0.0.2", "date": "2026-05-26T06:18:37.000Z", "commit": "63fdd47db29cfc589237ff67350de3aea76ea540", "fileid": "5c12b7130726d110e3abbe15e305c0067235951118465a1c4e4c40da43c1739b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mkajano/actions/runs/26435490899" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.2", "date": "2026-05-26T06:14:06.000Z", "commit": "63fdd47db29cfc589237ff67350de3aea76ea540", "fileid": "f0914fa93784ba7eba71f1b378ba91389292dd5e8ac6ab89aad2782ffe0d67e5", "status": "success", "buildurl": "https://github.com/r-universe/mkajano/actions/runs/26435490899" }, { "r": "4.7.0", "os": "win", "version": "0.0.2", "date": "2026-05-26T06:13:15.000Z", "commit": "63fdd47db29cfc589237ff67350de3aea76ea540", "fileid": "6c297f19f6e5b00ddcb8af7e5e721f5c73f6cf4472195f96ecc7be84a7c1d19d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mkajano/actions/runs/26435490899" }, { "r": "4.5.3", "os": "win", "version": "0.0.2", "date": "2026-05-26T06:13:25.000Z", "commit": "63fdd47db29cfc589237ff67350de3aea76ea540", "fileid": "12636172d4b7c9329578ee7b605bffce34c86f998df6a2596573c9fac8e5f787", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mkajano/actions/runs/26435490899" }, { "r": "4.6.0", "os": "win", "version": "0.0.2", "date": "2026-05-26T06:13:22.000Z", "commit": "63fdd47db29cfc589237ff67350de3aea76ea540", "fileid": "93289281582e38e6276de776cfc079700974f0fe7f0c6f948800adf0d4a6891a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mkajano/actions/runs/26435490899" } ] }