Tools for investigating RNA-Seq


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Documentation for package ‘sleuth’ version 0.30.0

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$<-.sleuth Extend internal '$<-' for sleuth object
basic_filter Basic row filter
design_matrix Extract design matrix
excluded_ids Excluded IDs in Kallisto object
extract_model Extract a model from a sleuth object
get_bootstraps Extract bootstrap for a specific transcript
get_bootstrap_summary bootstrap summary
get_col Get a data.frame from all kallisto objects
is_kallisto_subset Is Kallisto Object Subsetted?
kallisto_table Get kallisto abundance table from a sleuth object
log_transform Natural log and offset transformation
models View which models have been fit
norm_factors Normalization factors
plot_bootstrap Plot bootstrap summary
plot_fld.kallisto Plot fragment length distribution
plot_fld.sleuth Plot fragment length distribution
plot_group_density Plot density
plot_loadings Plot Loadings and Interpretations
plot_ma MA plot
plot_mean_var Mean-variance relationship
plot_pca Plot PCA
plot_pc_variance Plot PC Variance
plot_qq QQ plot
plot_sample_density Plot sample density
plot_sample_heatmap Plot sample heatmap
plot_scatter Sample to sample scatter plot
plot_transcript_heatmap Plot clustered heatmap
plot_vars Plot technical variance versus observed variance
plot_volcano Plot volcano plot
print.sleuth_model Print sleuth model
read_kallisto Read kallisto output
read_kallisto_h5 Read a kallisto object from an HDF5 file
read_kallisto_tsv Read kallisto plaintext output
sleuth_deploy deploy a sleuth object
sleuth_fit Fit a measurement error model
sleuth_gene_table Create a gene table from a sleuth object
sleuth_live Interactive sleuth visualization with Shiny
sleuth_live_settings settings for sleuth_live
sleuth_load load a sleuth object
sleuth_lrt sleuth likelihood ratio test
sleuth_prep Constructor for a 'sleuth' object
sleuth_results Extract Wald or Likelihood Ratio test results from a sleuth object
sleuth_save save a sleuth object
sleuth_to_matrix Convert a sleuth object to matrix
sleuth_wt Wald test for a sleuth model
subset_kallisto Subset a kallisto object
transcripts_from_gene Get the names of the transcripts associated to a gene
transform_fun_counts<- Change sleuth transform counts function
transform_fun_tpm<- Change sleuth transform TPM function
transform_status Check Transform Sync Status of Sleuth Fits
write_kallisto_hdf5 Write a kallisto object to HDF5