Man pages for pachterlab/sleuth
Tools for investigating RNA-Seq

basic_filterBasic row filter
cash-set-.sleuthExtend internal '$<-' for sleuth object
design_matrixExtract design matrix
excluded_idsExcluded IDs in Kallisto object
extract_modelExtract a model from a sleuth object
gene_from_geneGet the gene ID using other gene identifiers
get_bootstrapsExtract bootstrap for a specific transcript
get_bootstrap_summarybootstrap summary
get_colGet a data.frame from all kallisto objects
is_kallisto_subsetIs Kallisto Object Subsetted?
kallisto_tableGet kallisto abundance table from a sleuth object
log_transformNatural log and offset transformation
modelsView which models have been fit
norm_factorsNormalization factors
plot_bootstrapPlot bootstrap summary
plot_fld.kallistoPlot fragment length distribution
plot_fld.sleuthPlot fragment length distribution
plot_group_densityPlot density
plot_loadingsPlot Loadings and Interpretations
plot_maMA plot
plot_mean_varMean-variance relationship
plot_pcaPlot PCA
plot_pc_variancePlot PC Variance
plot_qqQQ plot
plot_sample_densityPlot sample density
plot_sample_heatmapPlot sample heatmap
plot_scatterSample to sample scatter plot
plot_transcript_heatmapPlot clustered heatmap
plot_varsPlot technical variance versus observed variance
plot_volcanoPlot volcano plot
print.sleuth_modelPrint sleuth model
read_kallistoRead kallisto output
read_kallisto_h5Read a kallisto object from an HDF5 file
read_kallisto_tsvRead kallisto plaintext output
sleuth_deploydeploy a sleuth object
sleuth_fitFit a measurement error model
sleuth_gene_tableCreate a gene table from a sleuth object
sleuth_liveInteractive sleuth visualization with Shiny
sleuth_live_settingssettings for sleuth_live
sleuth_loadload a sleuth object
sleuth_lrtsleuth likelihood ratio test
sleuth_prepConstructor for a 'sleuth' object
sleuth_resultsExtract Wald or Likelihood Ratio test results from a sleuth...
sleuth_savesave a sleuth object
sleuth_to_matrixConvert a sleuth object to matrix
sleuth_wtWald test for a sleuth model
subset_kallistoSubset a kallisto object
transcripts_from_geneGet the names of the transcripts associated to a gene
transform_fun_counts-setChange sleuth transform counts function
transform_fun_tpm-setChange sleuth transform TPM function
transform_statusCheck Transform Sync Status of Sleuth Fits
write_kallisto_hdf5Write a kallisto object to HDF5
pachterlab/sleuth documentation built on June 30, 2018, 1:14 p.m.