mspms-package	mspms-package
%>%	pipe
add_cleavages	add_cleavages
add_peptide_data	add_peptide_data
all_possible_8mers_from_228_library	all_possible_8mers_from_228_library
calculate_all_cleavages	calculate_all_cleavages
calc_AA_count_of_motif	calc_AA_count_of_motif
calc_AA_fc	calc_AA_fc
calc_AA_motif_zscore	calc_AA_motif_zscore
calc_AA_percent_difference	calc_AA_percent_difference
calc_AA_prop_of_motif	calc_AA_prop_of_motif
calc_limma_contrasts	calc_limma_contrasts
calc_limma_design_matrix	calc_limma_design_matrix
calc_per_samples_library_nd	calc_per_samples_library_nd
calc_sig_zscores	calc_sig_zscores
check_file_is_valid_fragpipe	check_file_is_valid_fragpipe
check_file_is_valid_pd	check_file_is_valid_pd
check_file_is_valid_peaks	check_file_is_valid_peaks
check_peptide_library	check_peptide_library
colData	colData
consolidate_cleavages	consolidate_cleavages
count_cleavages_per_pos	count_cleavages_per_pos
cterm_cleavage	cterm_cleavage
generate_report	generate_report
icelogo_col_scheme	icelogo_col_scheme
limma_stats	limma_stats
load_colData	load_colData
log2fc_t_test	log2fc_t_test
log2fc_t_test_data	log2fc_t_test_data
mspms	mspms-package
mspms_log2fc	mspms_log2fc
mspms_tidy	mspms_tidy
mspms_tidy_data	mspms_tidy_data
mspms_t_tests	mspms_t_tests
nterm_cleavage	nterm_cleavage
peaks_prepared_data	peaks_prepared_data
peptide_library	peptide_library
plot_all_icelogos	plot_all_icelogos
plot_cleavages_per_pos	plot_cleavages_per_pos
plot_heatmap	plot_heatmap
plot_icelogo	plot_icelogo
plot_nd_peptides	plot_nd_peptides
plot_pca	plot_pca
plot_qc_check	plot_qc_check
plot_time_course	plot_time_course
plot_volcano	plot_volcano
prepared_to_qf	prepared_to_qf
prepare_fc	prepare_fc
prepare_for_PCA	prepare_for_PCA
prepare_fragpipe	prepare_fragpipe
prepare_icelogo_data	prepare_icelogo_data
prepare_pd	prepare_pd
prepare_peaks	prepare_peaks
prepare_qc_check_data	prepare_qc_check_data
prepare_sig_p_dif	prepare_sig_p_dif
processed_qf	processed_qf
process_qf	process_qf
remaining_cd_names	remaining_cd_names
rlog2	rlog2
