Man pages for ecnuzdd/PhosMap
A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

analysis_deps_anovaDifferential expression analysis using ANOVA
analysis_deps_limmaDifferential expression analysis using limma.
analysis_deps_samDifferential expression analysis using SAM
BRAFiBRAFi data on quantification proteomics
check_mea_inputCheck input for motif enrichment analysis (mea)
compute_ksescomputing kinase-substrate enrichment score
construct_pwmConstruct position weight matrix
extract_psites_scoreCreate R code to call python for parsering mascot xml.
fore_seq_to_motifConvert the list that consists of motifs and the...
formatted_output_mef_resultsOutput formatted sequences in foreground that are mapped to...
generate_psites_score_fileGenerate peptide identification files with psites scores.
get_aligned_seq_for_meaTaking S/T/Y as the center, align sequence to fasta library...
get_colors_for_discrete_valueGenerate custom colors from discrete values for heatmap.
get_combined_data_frameGet a data frame mapped GI number to Gene Symbol.
get_df_with_AAs_iGet data frame of amino acide sequences for a protein.
get_file_info_from_dirGet data lists from and corresponding file ids.
get_file_suffixGet sufffix of input file.
get_filtered_dfGet filtered data frame based on the Mascot and reference...
get_foreground_df_to_motifsGet filtered foreground data frame that its aligned sequences...
get_foreground_seq_to_motifsGet motifs and their corresponding aligned sequences form...
get_global_background_dfGet background data frame (fasta library from Refseq).
get_ka_by_mean_or_mlrComputing kinase activity using mean value and multiple...
get_ksea_regulons_infoGet informational data frame by combining result from all...
get_ksea_result_listKinase activity analysis based on known and predicted...
get_ksescomputing kinase-substrate enrichment significance (pvalue)
get_list_with_filted_sitesFilter phosphorylation sites.
get_merged_phospho_dfGet merged data frame with phospho-peptides.
get_modification_indexGet index of modifications in protein sequence.
get_motif_analysis_summaryGet summary result of motif analysis for specific input
get_motifs_listMotif enrichment using rmotifx.
get_normalized_data_FOT5Normailization on basis of sum
get_normalized_data_of_psitesTo normalize data and filter data only including...
get_substrate_expr_dfGet a data frame only containing kinase inferred by KSEA
get_summary_from_kseaGet a data frame only containing inforamtion of kinase...
get_summary_with_unique_sitesAssign psites to protein sequence.
get_unique_AAs_i_dfGet data frame without redundancy.
helloHello, world!
keep_psites_with_max_in_topXKeep psites whose row maximum is top N (percentage).
mea_based_on_backgroundMotif enrichment based on global background (fasta library...
merge_profiling_file_from_FirmianaMerge profiling files downloaded from Firmiana.
motif_data_frame_to_sequenceConvert data frame of motif to the sequence pattern
normalize_nopair_ctrl_by_colFor data without pairs but with control, normalize them to...
normalize_nopair_noctrl_by_colmedFor data without pairs and control, normalize them to the...
normalize_phos_data_to_profilingNormalize phospho-data to profiling
normalize_to_PairFor data with pairs, normalize them to the sample with flag...
plot_seqlogoPlot sequence logo based on list that consist of motifs and...
pre_process_filter_psitesGet peptides data frame passed phosphorylation sites quality...
seach_motif_patternConvert data frame of motif to the sequence pattern
visualization_deps_with_scatterVisualize differentially expressed results with scatter
visualization_fuzzyclusterVisualize results from fuzzy clusters with line chart
visualization_with_simple_pcaA simple PCA plot.
visualization_with_simple_tsneA simple t-SNE plot.
write_csv_pep_seq_confWrite data to specific direction with CSV format.
ecnuzdd/PhosMap documentation built on Jan. 10, 2019, 10:39 p.m.