assemble_report-seaMass_sigma-method | Generate html report |
delta_control-class | Control parameters for seaMass-Δ |
dinaka | Probability density function of an inverse nakagami... |
dist_inaka | fit inverse nakagami distribution with fitdistrplus, note our... |
dist_lst | fit location-scale t distribution with fitdistrplus |
dist_normal | fit normal distribution with fitdistrplus |
dist_normal_robust | summarise using median/mad |
dist_samples_inaka | fit scaled inverse chi distribution |
dist_samples_lst | fit location-scale t distribution |
dist_samples_lst_ash | fit location-scale t distribution for ash (minimum df = 2) |
dist_samples_normal | fit normal distribution with fitdistrplus |
dist_samples_robust_normal | fit normal distribution with fitdistrplus |
dist_sf_with_fixed_df1_fitdistrplus | fit scaled F distribution with per-datapoint fixed df1 with... |
dlst | Probability density function of a location-scale t... |
generate_markdown-seaMass-method | Generate Rmarkdown for figure |
import_DIANN | Import DIA-NN data |
import_MaxQuant | Import MaxQuant LF data |
import_MaxQuant_evidence0 | Import MaxQuant LF data |
import_MaxQuant_peptides | Import MaxQuant LF data |
import_MSqRob | Import MaxQuant LF data |
import_MSstats | Import data outputed by an MSstats import routine |
import_OpenSWATH | Import OpenSWATH data |
import_Progenesis | Import Waters Progenesis data |
import_ProteinPilot | Import SCIEX ProteinPilot data |
import_ProteomeDiscoverer | Import Thermo ProteomeDiscoverer data |
lingofy-seaMass-method | Convert to local lingo |
new_assay_design | Specify study design for imported dataset |
pinaka | Cumulative distribution function (CDF) of an inverse nakagami... |
plot_assay_stdevs-seaMass_sigma-method | #' @import data.table #' @export #' @include generics.R... |
plot_assay_stdevs-sigma_block-method | #' @import data.table #' @export #' @include generics.R... |
plot_fdr-seaMass_delta-method | Add together two numbers. |
plot_pr-seaMass_delta-method | Precision-Recall plot |
plot_robust_pca-seaMass-method | Plot robust PCA fit |
plot_volcano-seaMass_delta-method | Volcano plot |
plst | Cumulative distribution function (CDF) of a location-scale t... |
qinaka | Quantile function (inverse CDF) of an inverse nakagami... |
qlst | Quantile function (inverse CDF) of a location-scale t... |
render_markdown-seaMass-method | Render Rmarkdown |
rhat | rhat |
robust_pca-seaMass-method | Robust PCA fit |
runs | Imported dataset run information |
schedule_local-class | Schedule seaMass to run locally |
schedule_pbs-class | Schedule seaMass to run on PBS |
schedule_sge-class | Schedule seaMass to run on SGE |
schedule_slurm-class | Schedule seaMass to run on SLURM |
seaMass-class | seaMass class |
seaMass_delta-class | seaMass-delta |
seaMass_group_quants-class | seaMass group quants class |
seaMass_sigma-class | seaMass-Σ |
seaMass_theta-class | seaMass-theta |
sigma_block-class | seaMass-Σ block |
sigma_control-class | Control parameters for seaMass-Σ |
squeeze_stdev | Our squeezeVar function - works for small DF unlike Limma... |
squeeze_stdev_limma | Limma squeezeVar function |
theta_block-class | seaMass-theta block |
theta_control-class | Control parameters for seaMass-theta |
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