Package to Perform High Throughput Biological Screening

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Documentation for package ‘ScreenR’ version 1.2.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

annotation_table	Table for the annotation of Barcode
barcode_lost	Count number of barcode lost
compute_data_table	Compute data Table
compute_metrics	Compute Metrics
compute_slope	Compute Slope of a Gene
count_mapped_reads	Count the number of mapped read
count_table	Table of the count table
create_edger_obj	Create edgeR Object
create_screenr_object	Create the ScreenR Object
filter_by_slope	Filter using the slope filter
filter_by_variance	Filter using the variance filter
find_camera_hit	Find Camera Hit
find_common_hit	Find common hit
find_roast_hit	Find Roast Hit
find_robust_zscore_hit	Title Find robust Z-score Hit
find_zscore_hit	Title Find Z-score Hit
get_annotation_table	Get ScreenR annotation table
get_annotation_table,screenr_object	Get ScreenR annotation table
get_annotation_table-method	Get ScreenR annotation table
get_count_table	Get ScreenR count table
get_count_table,screenr_object	Get ScreenR count table
get_count_table-method	Get ScreenR count table
get_data_table	Get ScreenR data_table
get_data_table,screenr_object	Get ScreenR data_table
get_data_table-method	Get ScreenR data_table
get_groups	Get ScreenR groups
get_groups,screenr_object	Get ScreenR groups
get_groups-method	Get ScreenR groups
get_normalized_count_table	Get ScreenR normalized_count_table
get_normalized_count_table,screenr_object	Get ScreenR normalized_count_table
get_normalized_count_table-method	Get ScreenR normalized_count_table
get_replicates	Get ScreenR replicates
get_replicates,screenr_object	Get ScreenR replicates
get_replicates-method	Get ScreenR replicates
mapped_reads	Mapped Reads
normalize_data	Normalize data
plot_barcode_hit	Plot barcode hit
plot_barcode_lost	Plot number of barcode lost
plot_barcode_lost_for_gene	Plot number of barcode lost for gene
plot_barcode_trend	Plot the trend over time of the barcodes
plot_boxplot	Plot Barcodes Hit
plot_common_hit	Plot common hit
plot_explained_variance	Plot the explained variance by the PC
plot_mapped_reads	Plot mapped reads
plot_mapped_reads_distribution	Plot the distribution of the mapped reads
plot_mds	Multidimensional Scaling Plot
plot_trend	Plot the trend hit gene
plot_zscore_distribution	Plot distribution Z-score
remove_all_zero_row	Remove rows that have zero count in all samples
screenr_object	Get ScreenR count table
screenr_object-class	Get ScreenR count table
set_annotation_table	Set ScreenR annotation table
set_annotation_table,screenr_object	Set ScreenR annotation table
set_annotation_table-method	Set ScreenR annotation table
set_count_table	Set ScreenR count table
set_count_table,screenr_object	Set ScreenR count table
set_count_table-method	Set ScreenR count table
set_data_table	Set ScreenR data_table
set_data_table,screenr_object	Set ScreenR data_table
set_data_table-method	Set ScreenR data_table
set_groups	Set ScreenR groups
set_groups,screenr_object	Set ScreenR groups
set_groups-method	Set ScreenR groups
set_normalized_count_table	Set ScreenR normalized_count_table
set_normalized_count_table,screenr_object	Set ScreenR normalized_count_table
set_normalized_count_table-method	Set ScreenR normalized_count_table
set_replicates	Set ScreenR replicates
set_replicates,screenr_object	Set ScreenR replicates
set_replicates-method	Set ScreenR replicates