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ddpcr  

Analysis and Visualization of Droplet Digital PCR in R and on the Web
View on CRAN: Click here


Download and install ddpcr package within the R console
Install from CRAN:
install.packages("ddpcr")

Install from Github:
library("remotes")
install_github("cran/ddpcr")

Install by package version:
library("remotes")
install_version("ddpcr", "1.15.2")



Attach the package and use:
library("ddpcr")
Maintained by
Dean Attali
[Scholar Profile | Author Map]
First Published: 2016-02-19
Latest Update: 2023-08-20
Description:
An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.
How to cite:
Dean Attali (2016). ddpcr: Analysis and Visualization of Droplet Digital PCR in R and on the Web. R package version 1.15.2, https://cran.r-project.org/web/packages/ddpcr. Accessed 29 Mar. 2025.
Previous versions and publish date:
1.0.1 (2016-02-19 14:51), 1.1.2 (2016-03-17 14:12), 1.3 (2016-06-05 17:38), 1.4 (2016-06-25 19:07), 1.5 (2016-08-03 20:32), 1.6 (2016-11-12 00:10), 1.8 (2017-06-24 08:00), 1.9 (2018-05-27 15:56), 1.11 (2019-01-03 16:10), 1.12 (2020-01-13 07:00), 1.13 (2020-02-28 08:20), 1.14 (2020-03-23 19:00), 1.15.1 (2023-04-03 00:10), 1.15 (2020-06-02 09:10)
Other packages that cited ddpcr R package
View ddpcr citation profile
Other R packages that ddpcr depends, imports, suggests or enhances
Complete documentation for ddpcr
Functions, R codes and Examples using the ddpcr R package
Some associated functions: WELL_ID_REGEX . analysis_complete . analyze . bind_df_ends . calc_negative_freq_simple . calculate_concentration . calculate_concentration_single . calculate_neg_freq_single . calculate_negative_freqs . capitalize . cat0 . check_step . classify_droplets . classify_droplets.pnpp_experiment . classify_droplets_single . classify_droplets_single.pnpp_experiment . classify_thresholds . cluster . cluster_name . clusters . col_to_num . custom_thresholds . ddpcr-package . ddpcr_plate . define_clusters.custom_thresholds . define_clusters.ddpcr_plate . define_clusters . define_clusters.pnpp_experiment . define_params.custom_thresholds . define_params.ddpcr_plate . define_params.fam_positive_pnpp . define_params.hex_positive_pnpp . define_params . define_params.pnpp_experiment . define_params.wildtype_mutant_pnpp . define_steps.custom_thresholds . define_steps.ddpcr_plate . define_steps . define_steps.pnpp_experiment . diff.point2d . err_msg . fam_positive_pnpp . get_col . get_empty_cutoff.ddpcr_plate . get_empty_cutoff . get_empty_cutoff.pnpp_experiment . get_filled_border . get_filled_drops . get_outlier_cutoff.ddpcr_plate . get_outlier_cutoff . get_row . get_single_well . get_wells_btwn . grapes-btwn-grapes . grapes-greater-than-grapes . has_signif_negative_cluster . has_step . hex_positive_pnpp . is_dir . is_dirty . is_empty_plate . is_file . is_range . is_well_success.ddpcr_plate . is_well_success . is_well_success.pnpp_experiment . launch . load_plate . local_maxima . local_minima . lol_to_df . mark_clusters . merge_dfs_overwrite_col . meta_var_name . move_back . move_front . msg . name . named_vec_to_df . new_plate . next_step . normalize_to_rds . num_to_col . num_to_row . other_dim . params . parent_plate_type.ddpcr_plate . parent_plate_type.default . parent_plate_type.fam_positive_pnpp . parent_plate_type.hex_positive_pnpp . parent_plate_type . parent_plate_type.wildtype_mutant_pnpp . plate_data-set . plate_data . plate_meta-set . plate_meta . plate_types . plot.custom_thresholds . plot.ddpcr_plate . plot.pnpp_experiment . plot.wildtype_mutant_pnpp . pnpp_experiment . point2d . positive_dim . positive_dim_var . positive_name . print.ddpcr_plate . quiet . range_list_to_vec . range_to_endpoints . range_to_seq . reclassify_droplets . reclassify_droplets.pnpp_experiment . reclassify_droplets_single . reclassify_droplets_single.pnpp_experiment . remove_empty.ddpcr_plate . remove_empty . remove_empty.pnpp_experiment . remove_failures.ddpcr_plate . remove_failures . remove_outliers.ddpcr_plate . remove_outliers . reset . row_to_num . sample_data . save_plate . set_default_params . status . step . step_begin . step_end . step_name . steps . subset.ddpcr_plate . thresholds . type . unanalyzed_clusters . variable_dim . variable_dim_var . warn_msg . well_info . wells_mutant . wells_negative . wells_positive . wells_success . wells_used . wells_wildtype . wildtype_mutant_pnpp . x_threshold . x_var . y_threshold . 
Some associated R codes: aaa.R . concentration.R . ddpcr-package.R . empty.R . failures.R . ignoreme.R . launch.R . outliers.R . pipe.R . plate-attribs.R . plate-extend.R . plate-print.R . plate-utils.R . plate.R . plot.R . pnpp_experiment-calculate_neg_freq.R . pnpp_experiment-classify.R . pnpp_experiment-empty.R . pnpp_experiment-failures.R . pnpp_experiment-filled.R . pnpp_experiment-plot.R . pnpp_experiment-reclassify.R . read.R . sample_data.R . save_load.R . subset.R . type-custom_thresholds.R . type-ddpcr_plate.R . type-fam_positive_pnpp.R . type-hex_positive_pnpp.R . type-pnpp_experiment.R . type-wildtype_mutant_pnpp.R . utils.R . zzz.R .  Full ddpcr package functions and examples
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