Man pages for hemoshear/assayr2
Tools for analyzing assay data
| activity_area | Calculate the activity area of a dose response curve |
| add_targets | Add targets to data.frame given a color legend |
| add_treatments | Add treatment labels to a data.frame with metadata |
| adj_activity_area | Calculate the error-ajusted activity area of a dose response... |
| analytes | Get character vector of analytes measured in MagPix assay |
| anyBaseToDecimal | Convert from anybase to decimal |
| apply_curve_matches | PureHoney helper function |
| assayr2-package | assayr2: a set of assay analysis tools |
| box_archive | Compress files needed to reproduce an analysis and upload to... |
| box_browse | Open a browser window via 'browseURL()' to look at a Box... |
| box_dl_pure_honey | Download raw data and layout files for a RNO experiment |
| box_fetch2 | A kind wrapper on 'boxr::box_fetch()'.' |
| box_push2 | A kind wrapper around 'boxr::box_push()" |
| check_and_match | A combination of 'check_values()' and 'closest_match()'. |
| check_names | Check a data frame against a white list for required names. |
| check_values | Check a data frame against a white list for required names. |
| chr_to_int | Convert characters to integers |
| closest_matches | Finds the value most similar to 'value' in 'values'. |
| coa | CoA data from PureHoney. |
| compileReport | Concatenate a set of PDFs |
| curve_matcher | PureHoney helper function |
| curves | Data related to DRC QC functions |
| curve_span | Curve span |
| der | Wrapper around 'dir()' |
| detect_outliers | Check for outliers using weights from Tukey's Biweight mean |
| detect_outliers_negative_cases | Data related to DRC QC functions |
| detect_outliers_positive_cases | Data related to DRC QC functions |
| drc_qc | Run QC check for a set of dose-response curves |
| drcs | Fitted dose response models |
| explorer_wl | White list for HST-Explorer |
| export_pdf | Export a plot list as a PDF |
| export_pngs | Export a plot list as PNGs |
| fct_sync | Make factor levels sync with those of a reference data.frame. |
| find_layout | Find common files on Box from R with a run ID. |
| find_plates | Find 96-well plate layouts in a data frame |
| flag_samples | A QC function for flagging technical replicate issues. |
| geom_mean | Geometric mean |
| geom_mean_se | Geometric standard error of the mean |
| geom_stat_crossbar | ggplot geoms to make it easy to plot the results of... |
| get_curves | Generate a data frame with y values in increments of a given... |
| get_curves_needing_qc | Get a table of dose-response curve data that should be... |
| getEC50 | Get the EC50 value of a 4-parmeter log-logistic function |
| getHillSlope | Get the Hill coefficient of a 4-parmeter log-logistic... |
| getLowerAsym | Get the y value of the lower asymptote in a 4-parmeter... |
| get_ph_metadata | Import meta data from various PureHoney files. |
| get_qc_warnings | Get QC warnings associated with a particular curve |
| get_tissue_conc | Estimate concentration in tissue |
| getUpperAsym | Get the y value of the upper asymptote in a 4-parmeter... |
| get_warning_message | Get warning message for a set of warning codes |
| get_warning_message_table | Get a table of mappings from warning codes to human-readable... |
| getYBounds | Get the bottom and top of a log-logistic curve in a given x... |
| ggheat | A heatmap summary for showing log2 fold changes. Built with... |
| insert_header_addin | Insert header for analysis script |
| inverse_predict | Generic function to do inverse prediction. |
| inverse_predict.drc | Inverse predict based on 'drc' model object. |
| inverse_predict.lm | Inverse predict based on a linear model object. |
| isobutyryl_curves | Data related to DRC QC functions |
| ll4_qc_warnings | Encode results of QC check in an integer warning code and... |
| ll4_robust_parameter_overlap | Overlapping confidence intervals for LL4 parameters (normal... |
| magpix_express_correct_data | Data related to magpix_express |
| make_c3c2 | Compute the C3/C2 ratio on Carntine data from PureHoney |
| make_cis | Generic function to do build confidence intervals. |
| make_fcs | Generic function to construct confidence intervals. |
| make_stats | A super-high level wrapper for building plot ready model... |
| melt_plate | Melt a data frame from plate format to long format |
| melt_plate_xlsx | Read xlsx data in plate format and convert to long format |
| mp_add_metadata | Add metadata to a MagPix object |
| mp_dotplot | Generate one or multiple dotplots for a single analyte in a... |
| mp_express | High level wrapper to process raw MagPix files. |
| mp_fit_standards | Fit a 4-parameter log-logistic model for each analyte in a... |
| mp_plot | Generate a list of standard curve plots, where each element... |
| mp_predict_concentrations | Predict analyte concentrations from observed intensities |
| mp_print | Print method for MagPix objects |
| new_zeros | Convert concentrations of zero to non-zero values in a dose... |
| nrmsd_qc | Calculate Normalized-Root-Mean-Square-Deviation (NRMSD) for... |
| nrmsd_qc_negative_cases | Data related to DRC QC functions |
| nrmsd_qc_positive_cases | Data related to DRC QC functions |
| nuc_join | PureHoney helper function |
| pal_magpix_flag | A color pallete for flagging MagPix samples |
| pal_pcr_flag | Get a named palette for coloring samples by flag in a PCR... |
| par_stats | Function to run makeStats in parallel. |
| pd | An abbreviation for position_dodge() |
| ph_color_pal | The color palette for isotopes in PureHoney experiments... |
| ph_fill_pal | The fill palette for isotopes in PureHoney experiments Colors... |
| poor_ic50_estimate | Check if an asymptote estimate for a 4-parameter log-logistic... |
| poor_ic50_estimate_negative_cases | Data related to DRC QC functions |
| poor_ic50_estimate_positive_cases | Data related to DRC QC functions |
| read_cfx | Generic parser for Biorad CFX thermocycler |
| read_color_layouts | Read color PCR layouts |
| read_device_layout | Read in a device layout from Box |
| read_discards | Extract sample identifiers from a file with discards from... |
| read_fluostar | Generic parser for data from the Omega FLUOStar plate... |
| read_generic | Universal assayr2 function template to read in tables. |
| read_layouts | A parser for plate maps |
| read_magpix | Parser for MagPix csv outputs |
| read_moldev | Parser for Molecular Devices scope output |
| read_ph_assay | Generic parser for PureHoney Assay layouts |
| read_ph_raw | PureHoney Assay Result Reader |
| read_smad | Read in SMAD quantification data post ImageJ analysis |
| reexports | Objects exported from other packages |
| register_labeller | Register a new function for creating treatment labels given a... |
| RMAX | Calculate the maximum response of a DRC |
| robustify_drc | Make a robust DRC estimate using a method based on Nguyen et... |
| run_qc_check | Wrapper to run entire QC check for a given machine |
| save_explorer_rds | A wrapper for saving PureHoney data for used in the Shiny... |
| serial_dilution | Make a vector of serially halved values. |
| tabla | Alternate version of 'table', with 'useNA = "ifany"' |
| theme_assayr | Complete theme for assayr2. |
| tx_run2warning_code | Get warning codes for a vector of run identifiers |
| unbounded_parameter_ci | Check if a parameter estimate is unbounded |
| unbounded_parameter_ci_test_case | Data related to DRC QC functions |
| unsaturated_curve | Check if curve is saturated |
| unsaturated_curve_negative_cases | Data related to DRC QC functions |
| unsaturated_curve_positive_cases | Data related to DRC QC functions |
| WES | Calculate the weighted Shannon entropy score (WES) |
