Files in qzhang503/proteoQ
Processing and Informatic Analysis of Mass Spectrometrirc Data
.Rbuildignore
.gitignore
.gitignore.swp
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/cluego_api.R
R/corrplots.R
R/datasets.R
R/dbs.R
R/funs.R
R/global.R
R/go.R
R/gsea.R
R/gspa.R
R/gsva.R
R/histo.R
R/hm.R
R/informatics.R
R/kin.R
R/lda.R
R/mds.R
R/metadata.R
R/nmf.R
R/normalization.R
R/outliers.R
R/pca.R
R/peptable.R
R/prntable.R
R/proteoQ.R
R/psmtable.R
R/purge.R
R/roadmap.R
R/sigtests.R
R/simulData.R
R/specialty.R
R/string.R
R/trends.R
R/utils.R
R/utils_proteom.R
R/volcanos.R
R/wrappers.R
R/zzz.R
README.html
README.md
data-raw/additional_sigtest_setups.R
data-raw/annotProteinAccession.R
data/aa_residues.rda
data/c2_msig_hs.rda
data/c2_msig_mm.rda
data/c2_msig_rn.rda
data/go_sets_hs.rda
data/go_sets_mm.rda
data/go_sets_rn.rda
data/kegg_sets_hs.rda
data/kegg_sets_mm.rda
data/kegg_sets_rn.rda
data/kinase_lookup.rda
data/kinsub_hs.rda
data/kinsub_mm.rda
data/kinsub_rn.rda
data/mart_hs.rda
data/mart_mm.rda
data/mart_rn.rda
data/mq_mods.rda
data/prn_annot_crap.rda
data/refseq_entrez_hs.rda
data/refseq_entrez_mm.rda
data/refseq_entrez_rn.rda
data/uniprot_entrez_hs.rda
data/uniprot_entrez_mm.rda
data/uniprot_entrez_rn.rda
data/uniprot_species.rda
images/installation/three_tier_expt_smry.png
images/peptide/corrplot/corr_pnnl.png
images/peptide/histogram/bi1_n_1.png
images/peptide/histogram/bi1_nac_scaley_no.png
images/peptide/histogram/bi1_nac_scaley_yes.png
images/peptide/histogram/bi1_z_1.png
images/peptide/histogram/bi1_z_mc_2.png
images/peptide/histogram/bi_cmbn_peptides.png
images/peptide/histogram/mixed_bed_3.png
images/peptide/histogram/pSTY_bi1_scaley_no.png
images/peptide/histogram/pSTY_bi1_scaley_yes.png
images/peptide/histogram/partial_refit.png
images/peptide/histogram/peptide_refw2.png
images/peptide/histogram/peptide_refw2w16.png
images/peptide/mds/eucdist_jhu.png
images/peptide/mds/jhu.png
images/peptide/mds/mds.png
images/peptide/mds/new_jhu.png
images/peptide/purge/bi1.png
images/peptide/purge/bi1_ptcv.png
images/protein/corrplot/corr_pnnl.png
images/protein/eucdist/interplex_errors.png
images/protein/gspa/all_sets.png
images/protein/gspa/gspa_connet.png
images/protein/gspa/gspa_redund.png
images/protein/gspa/show_human_redundancy.png
images/protein/heatmap/kinase.png
images/protein/heatmap/mostly_na_vals.png
images/protein/heatmap/protein.png
images/protein/histogram/bi1_z.png
images/protein/histogram/bi1_z_npep10.png
images/protein/model/raneff_models.png
images/protein/nmf/bi_r5_coef_rank5.png
images/protein/nmf/bi_r5_con_rank5.png
images/protein/pca/cent.png
images/protein/pca/d3.png
images/protein/pca/nocent.png
images/protein/pca/nocent_2.png
images/protein/pca/sub_cent.png
images/protein/pca/sub_nocent.png
images/protein/purge/prn_sd_af.png
images/protein/purge/prn_sd_bf.png
images/protein/trend/bi_nclust6.png
images/protein/trend/cl4_nclust6.png
images/protein/trend/prn_trend_n6.png
images/protein/volcplot/batches.png
images/protein/volcplot/gspa_batch_geomean.png
images/protein/volcplot/gspa_batch_limma.png
images/protein/volcplot/hs_SMID_BREAST_CANCER_BASAL_DN.png
images/protein/volcplot/hs_SMID_BREAST_CANCER_LUMINAL_A_DN.png
images/protein/volcplot/hs_SMID_BREAST_CANCER_LUMINAL_B_UP.png
images/protein/volcplot/locations.png
images/psm/purge/psm_maxcv_purge.png
images/psm/purge/psm_no_purge.png
images/psm/purge/psm_qt_purge.png
inst/extdata/cpp1.R
inst/extdata/examples/KinSub_.R
inst/extdata/examples/PSM2Pep_.R
inst/extdata/examples/Pep2Prn_.R
inst/extdata/examples/load_expts_.R
inst/extdata/examples/mergePep_.R
inst/extdata/examples/normPSM_.R
inst/extdata/examples/normPep_.R
inst/extdata/examples/normPrn_.R
inst/extdata/examples/prepEntrez_.R
inst/extdata/examples/prnCorr_.R
inst/extdata/examples/prnEucDist_.R
inst/extdata/examples/prnGSEA_.R
inst/extdata/examples/prnGSPAHM_.R
inst/extdata/examples/prnGSPA_.R
inst/extdata/examples/prnGSVA_.R
inst/extdata/examples/prnHM_.R
inst/extdata/examples/prnHist_.R
inst/extdata/examples/prnLDA_.R
inst/extdata/examples/prnMDS_.R
inst/extdata/examples/prnNMF_.R
inst/extdata/examples/prnPCA_.R
inst/extdata/examples/prnSig_.R
inst/extdata/examples/prnString_.R
inst/extdata/examples/prnTrend_.R
inst/extdata/examples/prnVol_.R
inst/extdata/examples/purgePSM_.R
inst/extdata/examples/purgePep_.R
inst/extdata/mascot_keys.xlsx
inst/extdata/master.xml
inst/extdata/peptide_keys.txt
inst/extdata/protein_keys.txt
inst/extdata/psm_keys.txt
inst/extdata/varargs.txt
inst/extdata/workflow_lfq_base.R
inst/extdata/workflow_tmt_base.R
inst/extdata/workflow_tmt_ext.R
man/Dixon_outliers.Rd
man/Grubbs_outliers.Rd
man/KinSubTest.Rd
man/PSM2Pep.Rd
man/Pep2Prn.Rd
man/Rosner_outliers.Rd
man/TMT_levels.Rd
man/TMT_plex.Rd
man/TMT_plex2.Rd
man/TMT_top_n.Rd
man/Uni2Entrez.Rd
man/aa_residues.Rd
man/add_col_rawfile.Rd
man/add_cols_at.Rd
man/add_custom_entrez.Rd
man/add_empai.Rd
man/add_entrez.Rd
man/add_entry_ids.Rd
man/add_fasta_attrs.Rd
man/add_mascot_pepseqmod.Rd
man/add_mascot_raw.Rd
man/add_maxquant_pepseqmod.Rd
man/add_mbr_psms.Rd
man/add_mean_dev.Rd
man/add_mod_conf.Rd
man/add_msfragger_pepseqmod.Rd
man/add_msgf_pepseqmod.Rd
man/add_n_pepexpz.Rd
man/add_pep_retsd.Rd
man/add_pepseqmod.Rd
man/add_prot_desc.Rd
man/add_prot_icover.Rd
man/add_quality_cols.Rd
man/add_refseq_gene.Rd
man/add_shared_genes.Rd
man/add_shared_prot_accs_mf.Rd
man/add_shared_sm_genes.Rd
man/add_sm_pepseqmod.Rd
man/aggrLFQs.Rd
man/aggrNumLCMS.Rd
man/aggrNums.Rd
man/aggrTopn.Rd
man/analNMF.Rd
man/analTrend.Rd
man/anal_KinSub.Rd
man/anal_pepNMF.Rd
man/anal_prnString.Rd
man/anal_prnTrend.Rd
man/annotKin.Rd
man/annotPSM.Rd
man/annotPeppos.Rd
man/annotPrn.Rd
man/annot_KinSub.Rd
man/annot_from_to.Rd
man/annot_stringdb.Rd
man/arrangers_in_call.Rd
man/assign_duppeps.Rd
man/batchPSMheader.Rd
man/byfile_gspahm.Rd
man/byfile_plotVolcano.Rd
man/byfml_gspahm.Rd
man/byfml_volcano.Rd
man/c2_msig_hs.Rd
man/c2_msig_mm.Rd
man/c2_msig_rn.Rd
man/calcPeptide.Rd
man/calcSD_Splex.Rd
man/calcTMTLabs.Rd
man/calc_avgpep.Rd
man/calc_cover.Rd
man/calc_lfq_log2r.Rd
man/calc_lfq_prnnums.Rd
man/calc_pep_retsd.Rd
man/calc_sd_fcts.Rd
man/calc_sd_fcts_psm.Rd
man/calc_tmt_prnnums.Rd
man/calclfqPepInts.Rd
man/calclfqPepNums.Rd
man/center_df.Rd
man/channelInfo.Rd
man/check_aes_length.Rd
man/check_channel_prefix.Rd
man/check_depreciated_args.Rd
man/check_dots.Rd
man/check_dup_unimods.Rd
man/check_dups_at_lcms_and_sid.Rd
man/check_empty_rows.Rd
man/check_exptfrac_raws.Rd
man/check_formalArgs.Rd
man/check_formalArgs2.Rd
man/check_frac_multipsms.Rd
man/check_ggplot_aes.Rd
man/check_gset_nms.Rd
man/check_lfq_exptraws.Rd
man/check_metadata_integers.Rd
man/check_mq_df.Rd
man/check_optional_cols.Rd
man/check_raws.Rd
man/check_required_cols.Rd
man/check_tmt126_row.Rd
man/check_tmt_chans_vs_levs.Rd
man/check_tmt_emptyids.Rd
man/check_tmt_mixplexes.Rd
man/check_tmt_nc.Rd
man/check_tmt_plex.Rd
man/check_tmt_rawfiles.Rd
man/check_tmt_ref.Rd
man/check_tmt_sampleids.Rd
man/check_unnamed_cols.Rd
man/checkdots_analTrend.Rd
man/cleanupPSM.Rd
man/cluego.Rd
man/cmbn_meta.Rd
man/colAnnot.Rd
man/concat_fml_dots.Rd
man/contain_str.Rd
man/cos_sim.Rd
man/count_pepmiss.Rd
man/count_phosphopeps.Rd
man/create_db_path.Rd
man/create_os_lookup.Rd
man/dblTrim.Rd
man/deduce_mod_indexes.Rd
man/dixon_test.Rd
man/dl_msig.Rd
man/env_where.Rd
man/extract_mq_ints.Rd
man/extract_psm_raws.Rd
man/extract_raws.Rd
man/filterData.Rd
man/filters_in_call.Rd
man/find_NorZ.Rd
man/find_abbr_species.Rd
man/find_delim.Rd
man/find_fit_nms.Rd
man/find_fn_bases.Rd
man/find_fn_exts.Rd
man/find_human_orthologs.Rd
man/find_int_cols.Rd
man/find_mascot_plex.Rd
man/find_mascot_psmraws.Rd
man/find_mascot_tmtplex.Rd
man/find_mascot_vmods.Rd
man/find_mf_psmraws.Rd
man/find_mod_indexesQ.Rd
man/find_mq_psmraws.Rd
man/find_n_comp.Rd
man/find_padding_pos.Rd
man/find_pep_pos.Rd
man/find_pq_psmraws.Rd
man/find_preceding_colnm.Rd
man/find_pri_df.Rd
man/find_prot_family_rows.Rd
man/find_psmQ_files.Rd
man/find_ratio_cols.Rd
man/find_search_engine.Rd
man/find_sec_df.Rd
man/find_shared_prots.Rd
man/find_sm_psmraws.Rd
man/fitKernelDensity.Rd
man/fixBrukerMGF.Rd
man/fml2mass.Rd
man/fml_gsea.Rd
man/fml_gspa.Rd
man/fmt_num_cols.Rd
man/fullVolcano.Rd
man/geom_lower_text.Rd
man/geom_table.Rd
man/get_col_types.Rd
man/get_full_entrez.Rd
man/get_gl_dat_dir.Rd
man/gg_imgname.Rd
man/gn_rollup.Rd
man/go_sets_hs.Rd
man/go_sets_mm.Rd
man/go_sets_rn.Rd
man/greedysetcover.Rd
man/grubbs_test.Rd
man/gsVolcano.Rd
man/gspaHM.Rd
man/gspaMap.Rd
man/gspaTest.Rd
man/gspa_colAnnot.Rd
man/gspa_summary_limma.Rd
man/gspa_summary_mean.Rd
man/gsvaTest.Rd
man/hdeduce_mod_indexes.Rd
man/hfind_fit_nms.Rd
man/hfind_shared_prots.Rd
man/hparse_fasta.Rd
man/hsubColnames.Rd
man/identical_dots.Rd
man/imputeNA.Rd
man/info_anal.Rd
man/ins_cols_after.Rd
man/is_all_nan.Rd
man/is_trivial_col.Rd
man/is_trivial_dbl.Rd
man/join_mgfs.Rd
man/kegg_sets_hs.Rd
man/kegg_sets_mm.Rd
man/kegg_sets_rn.Rd
man/kinase_lookup.Rd
man/kinsub_hs.Rd
man/kinsub_mm.Rd
man/kinsub_rn.Rd
man/labEffPSM.Rd
man/lgl_cleanup.Rd
man/list_to_dataframe.Rd
man/lm_gspa.Rd
man/lm_summary.Rd
man/load_craps.Rd
man/load_dbs.Rd
man/load_expts.Rd
man/load_fasta.Rd
man/load_ls_group.Rd
man/load_prior.Rd
man/load_psmC.Rd
man/load_stringdbs.Rd
man/locate_outliers.Rd
man/make_cls.Rd
man/make_frac_smry.Rd
man/make_gct.Rd
man/make_mascot_intensities.Rd
man/make_mascot_ratios.Rd
man/make_mq_meta.Rd
man/make_mq_meta2.Rd
man/map_essential.Rd
man/map_peps_prots.Rd
man/map_to_entrez.Rd
man/map_to_entrez_os_name.Rd
man/mart_hs.Rd
man/mart_mm.Rd
man/mart_rn.Rd
man/mascot_refseq2uniprot.Rd
man/match_call_arg.Rd
man/match_fmls.Rd
man/match_gset_nms.Rd
man/match_logi_gv.Rd
man/match_pepSig_scale_log2r.Rd
man/match_prnSig_scale_log2r.Rd
man/maxquant_refseq2uniprot.Rd
man/mcPSM.Rd
man/med_summarise_keys.Rd
man/mergePep.Rd
man/mfixBrukerMGF.Rd
man/mmbr_psms.Rd
man/model_onechannel.Rd
man/mprocBrukerMGF.Rd
man/mq_mods.Rd
man/msubsetBrukerMGF.Rd
man/my_complete_cases.Rd
man/my_custom_cor.Rd
man/my_dist.Rd
man/my_geomean.Rd
man/my_padj.Rd
man/my_pheatmap.Rd
man/my_sum_n.Rd
man/my_tolower.Rd
man/my_union.Rd
man/my_upper.Rd
man/my_which_max.Rd
man/n_LCMS.Rd
man/n_TMT_sets.Rd
man/na_genes_by_acc.Rd
man/na_single_lfq.Rd
man/na_species_by_org.Rd
man/na_zeroIntensity.Rd
man/names_pos-set.Rd
man/newColnames.Rd
man/nmix_params.Rd
man/normMulGau.Rd
man/normPSM.Rd
man/normPep_Mplex.Rd
man/normSD.Rd
man/not_all_NA.Rd
man/not_all_nan.Rd
man/not_all_zero.Rd
man/not_allzero_rows.Rd
man/ok_existing_params.Rd
man/ok_file_ncomp.Rd
man/ok_min_size.Rd
man/order_mascot_psm_cols.Rd
man/order_psm_cols.Rd
man/p_dixon.Rd
man/p_grubbs.Rd
man/pad_grp_samples.Rd
man/pad_mascot_channels.Rd
man/pad_mascot_fields.Rd
man/pad_mf_channels.Rd
man/pad_mq_channels.Rd
man/pad_psm_fields.Rd
man/pad_sm_channels.Rd
man/pad_tmt_channels.Rd
man/parse_acc.Rd
man/parse_col_select.Rd
man/parse_fasta.Rd
man/parse_filename.Rd
man/pep_mq_lfq.Rd
man/pep_mq_lfq2.Rd
man/pep_to_prn.Rd
man/plotCorr.Rd
man/plotEucDist.Rd
man/plotHM.Rd
man/plotHisto.Rd
man/plotLDA.Rd
man/plotMDS.Rd
man/plotNMFCoef.Rd
man/plotNMFCon.Rd
man/plotNMFmeta.Rd
man/plotPCA.Rd
man/plotTrend.Rd
man/plotVolcano.Rd
man/plot_corr_sub.Rd
man/plot_metaNMF.Rd
man/plot_pepNMFCon.Rd
man/plot_prnTrend.Rd
man/plot_venn.Rd
man/pre_mq_meta.Rd
man/prepDM.Rd
man/prepFml.Rd
man/prepGO.Rd
man/prepMSig.Rd
man/prepString.Rd
man/prep_folded_tdata.Rd
man/prep_fraction_scheme.Rd
man/prep_gspa.Rd
man/prep_label_scheme.Rd
man/prep_range.Rd
man/prnCorr_logFC.Rd
man/prnEucDist.Rd
man/prnGSEA.Rd
man/prnGSPA.Rd
man/prnGSPAHM.Rd
man/prnGSVA.Rd
man/prnHM.Rd
man/prnHist.Rd
man/prnLDA.Rd
man/prnMDS.Rd
man/prnPCA.Rd
man/prnSig.Rd
man/prnVol.Rd
man/prn_annot_crap.Rd
man/procBrukerMGF.Rd
man/procBrukerMGF_v1.Rd
man/procMSGFmods.Rd
man/procPSMs.Rd
man/procTMT0.Rd
man/proc_gaf.Rd
man/proc_gmt.Rd
man/proc_obo.Rd
man/proteoQ.Rd
man/proteo_hm.Rd
man/psm_mcleanup.Rd
man/psm_mpurge.Rd
man/psm_msplit.Rd
man/psm_to_pep.Rd
man/purgePSM.Rd
man/purgePep.Rd
man/purge_by_cv.Rd
man/purge_by_n.Rd
man/purge_by_qt.Rd
man/pval_complete_cases.Rd
man/q_dixon.Rd
man/q_grubbs.Rd
man/q_table.Rd
man/ratio_toCtrl.Rd
man/read_fasta.Rd
man/read_metadata.Rd
man/recheck_tmt_channels.Rd
man/recur_flatten.Rd
man/refseq_entrez_hs.Rd
man/refseq_entrez_mm.Rd
man/refseq_entrez_rn.Rd
man/reload_expts.Rd
man/reloc_col.Rd
man/reloc_col_after.Rd
man/reloc_col_after_first.Rd
man/reloc_col_after_last.Rd
man/reloc_col_before.Rd
man/reloc_col_before_first.Rd
man/reloc_col_before_last.Rd
man/reorderCols.Rd
man/reorderCols2.Rd
man/reorder_files.Rd
man/rep_ls_groups.Rd
man/replace_NorZ_names.Rd
man/replace_by_rowone.Rd
man/replace_cols_at.Rd
man/replace_empty_with_na.Rd
man/replace_na_genes.Rd
man/replace_na_with_empty.Rd
man/replace_trivial_with_na.Rd
man/rmPSMHeaders.Rd
man/rm_cols_mqpsm.Rd
man/rm_fully_empty_tmt_sets.Rd
man/rm_pval_whitespace.Rd
man/rm_sglval_cols.Rd
man/rowVars.Rd
man/rptr_violin.Rd
man/save_call.Rd
man/scoreEucDist.Rd
man/scoreLDA.Rd
man/scoreMDS.Rd
man/scorePCA.Rd
man/sd_violin.Rd
man/setHMColor.Rd
man/setHMlims.Rd
man/set_cutpoints.Rd
man/set_cutpoints2.Rd
man/set_dat_dir.Rd
man/set_db_outname.Rd
man/set_ggsave_dots.Rd
man/set_mascot_colnms.Rd
man/sigTest.Rd
man/simple_label_scheme.Rd
man/simulUniprotPSM.Rd
man/single_mq_prntable.Rd
man/smbr_psms.Rd
man/sort_tmt_lcms.Rd
man/sp_lookup.Rd
man/sp_lookup_Ul.Rd
man/sp_lookup_go.Rd
man/spline_coefs.Rd
man/splitPSM.Rd
man/splitPSM_mf.Rd
man/splitPSM_mq.Rd
man/splitPSM_msgf.Rd
man/splitPSM_pq.Rd
man/splitPSM_sm.Rd
man/spreadPepNums.Rd
man/standPep.Rd
man/standPrn.Rd
man/stringTest.Rd
man/subsetBrukerMGF.Rd
man/subset_fasta.Rd
man/subset_keepattr.Rd
man/subset_volcano_df.Rd
man/sumdnorm.Rd
man/summ_venn.Rd
man/syn_empty_channels.Rd
man/taxid_lookup.Rd
man/taxid_lookup_rev.Rd
man/tmt_wtmean.Rd
man/to_complete_cases.Rd
man/to_csv_.Rd
man/to_linfc.Rd
man/triv_optcols_at_empty.Rd
man/uniprot_entrez_hs.Rd
man/uniprot_entrez_mm.Rd
man/uniprot_entrez_rn.Rd
man/uniprot_species.Rd
man/update_frac_smry.Rd
man/update_nodes.Rd
man/use_mq_peptable.Rd
man/vararg_secmsg.Rd
man/write_excel_wb.Rd
man/write_fasta.Rd
man/write_metadata.Rd
src/.gitignore
src/code.cpp
vignettes/.gitignore
vignettes/README.Rmd
vignettes/README.md
vignettes/images/installation/three_tier_expt_smry.png
vignettes/images/norm_diag_files/d3-4.5.0/LICENSE
vignettes/images/norm_diag_files/d3-4.5.0/d3.min.js
vignettes/images/norm_diag_files/diagonalNetwork-binding-0.4/diagonalNetwork.js
vignettes/images/norm_diag_files/htmlwidgets-1.5.1/htmlwidgets.js
vignettes/images/peptide/corrplot/corr_pnnl.png
vignettes/images/peptide/histogram/bi1_n_1.png
vignettes/images/peptide/histogram/bi1_nac_scaley_no.png
vignettes/images/peptide/histogram/bi1_nac_scaley_yes.png
vignettes/images/peptide/histogram/bi1_z_1.png
vignettes/images/peptide/histogram/bi1_z_mc_2.png
vignettes/images/peptide/histogram/bi_cmbn_peptides.png
vignettes/images/peptide/histogram/mixed_bed_3.png
vignettes/images/peptide/histogram/pSTY_bi1_scaley_no.png
vignettes/images/peptide/histogram/pSTY_bi1_scaley_yes.png
vignettes/images/peptide/histogram/partial_refit.png
vignettes/images/peptide/histogram/peptide_refw2.png
vignettes/images/peptide/histogram/peptide_refw2w16.png
vignettes/images/peptide/mds/eucdist_jhu.png
vignettes/images/peptide/mds/jhu.png
vignettes/images/peptide/mds/mds.png
vignettes/images/peptide/mds/new_jhu.png
vignettes/images/peptide/purge/bi1.png
vignettes/images/peptide/purge/bi1_ptcv.png
vignettes/images/protein/corrplot/corr_pnnl.png
vignettes/images/protein/eucdist/interplex_errors.png
vignettes/images/protein/gspa/all_sets.png
vignettes/images/protein/gspa/gspa_connet.png
vignettes/images/protein/gspa/gspa_redund.png
vignettes/images/protein/gspa/show_human_redundancy.png
vignettes/images/protein/heatmap/kinase.png
vignettes/images/protein/heatmap/mostly_na_vals.png
vignettes/images/protein/heatmap/protein.png
vignettes/images/protein/histogram/bi1_z.png
vignettes/images/protein/histogram/bi1_z_npep10.png
vignettes/images/protein/model/raneff_models.png
vignettes/images/protein/nmf/bi_r5_coef_rank5.png
vignettes/images/protein/nmf/bi_r5_con_rank5.png
vignettes/images/protein/pca/cent.png
vignettes/images/protein/pca/d3.png
vignettes/images/protein/pca/nocent.png
vignettes/images/protein/pca/nocent_2.png
vignettes/images/protein/pca/sub_cent.png
vignettes/images/protein/pca/sub_nocent.png
vignettes/images/protein/purge/prn_sd_af.png
vignettes/images/protein/purge/prn_sd_bf.png
vignettes/images/protein/trend/bi_nclust6.png
vignettes/images/protein/trend/cl4_nclust6.png
vignettes/images/protein/trend/prn_trend_n6.png
vignettes/images/protein/volcplot/batches.png
vignettes/images/protein/volcplot/gspa_batch_geomean.png
vignettes/images/protein/volcplot/gspa_batch_limma.png
vignettes/images/protein/volcplot/hs_SMID_BREAST_CANCER_BASAL_DN.png
vignettes/images/protein/volcplot/hs_SMID_BREAST_CANCER_LUMINAL_A_DN.png
vignettes/images/protein/volcplot/hs_SMID_BREAST_CANCER_LUMINAL_B_UP.png
vignettes/images/protein/volcplot/locations.png
vignettes/images/psm/purge/psm_maxcv_purge.png
vignettes/images/psm/purge/psm_no_purge.png
vignettes/images/psm/purge/psm_qt_purge.png
