API for pachterlab/sleuth
Tools for investigating RNA-Seq

Global functions
$<-.sleuth Man page
add_test Source code
adf Source code
aggregate_bootstrap Source code
apply_all_pairs Source code
as_df Source code
basic_filter Man page Source code
bias_table Source code
bias_table.kallisto Source code
bias_table.sleuth Source code
bootstrap2mat Source code
bs_sigma_summary Source code
check_kal_pack Source code
check_norm_status Source code
check_num_cores Source code
check_quant_mode Source code
check_target_mapping Source code
compute_likelihood Source code
counts_to_fpkm Source code
counts_to_tpm Source code
covar_beta Source code
dcast_bootstrap Source code
dcast_bootstrap.kallisto Source code
dcast_bootstrap.sleuth Source code
design_matrix Man page Source code
dot Source code
enclosed_brush Source code
excluded_ids Man page Source code
extract_model Man page Source code
filter_df_all_groups Source code
filter_df_by_groups Source code
gene_from_gene Man page Source code
gene_summary Source code
get_bootstrap_summary Man page Source code
get_bootstraps Man page Source code
get_bootstraps.kallisto Source code
get_bootstraps.sleuth Source code
get_col Man page Source code
get_kallisto_path Source code
get_likelihood Source code
get_quantile Source code
get_test Source code
gtf_attributes_to_gene_trans Source code
gtf_gene_names Source code
h5check Source code
head.kallisto Source code
is_kallisto_subset Man page Source code
is_kallisto_subset.kallisto Source code
is_kallisto_subset.sleuth Source code
jsd Source code
kallisto_table Man page Source code
kld Source code
kv_vec_to_df Source code
likelihood_exists Source code
list_all_tests Source code
list_tests Source code
log_transform Man page Source code
me_heteroscedastic_by_row Source code
me_model Source code
me_model_by_row Source code
me_white_model Source code
me_white_var Source code
melt_bootstrap Source code
melt_bootstrap_sleuth Source code
model_exists Source code
models Man page Source code
models.sleuth Source code
models.sleuth_model Source code
msg Source code
norm_factors Man page Source code
normalize_bootstrap Source code
obs_to_matrix Source code
plot_bootstrap Man page Source code
plot_fld Source code
plot_fld.kallisto Man page Source code
plot_fld.sleuth Man page Source code
plot_group_density Man page Source code
plot_loadings Man page Source code
plot_ma Man page Source code
plot_mean_var Man page Source code
plot_pc_variance Man page Source code
plot_pca Man page Source code
plot_qq Man page Source code
plot_sample_density Man page Source code
plot_sample_heatmap Man page Source code
plot_scatter Man page Source code
plot_transcript_heatmap Man page Source code
plot_vars Man page Source code
plot_volcano Man page Source code
print.kallisto Source code
print.sleuth Source code
print.sleuth_model Man page Source code
process_bootstrap Source code
propagate_transcript_filter Source code
read_bootstrap_hdf5 Source code
read_bootstrap_mat Source code
read_gtf Source code
read_kallisto Man page Source code
read_kallisto_h5 Man page Source code
read_kallisto_tsv Man page Source code
reads_per_base_transform Source code
sample_bootstrap Source code
shrink_df Source code
sleuth_deploy Man page Source code
sleuth_fit Man page Source code
sleuth_gene_table Man page Source code
sleuth_live Man page Source code
sleuth_live_settings Man page Source code
sleuth_load Man page Source code
sleuth_lrt Man page Source code
sleuth_prep Man page Source code
sleuth_results Man page Source code
sleuth_save Man page Source code
sleuth_summarize_bootstrap Source code
sleuth_summarize_bootstrap_col Source code
sleuth_to_matrix Man page Source code
sleuth_wt Man page Source code
sliding_window_grouping Source code
spread_abundance_by Source code
subset_kallisto Man page Source code
subset_kallisto.kallisto Source code
subset_kallisto.sleuth Source code
summarize_bootstrap Source code
summary.sleuth Source code
test_exists Source code
tests Source code
tests.sleuth Source code
tpm_to_alpha Source code
trans_to_genes_from_gtf Source code
transcripts_from_gene Man page Source code
transform_fun_counts<- Man page
transform_fun_tpm<- Man page
transform_status Man page Source code
transform_status.sleuth Source code
transform_status.sleuth_model Source code
write_kallisto_hdf5 Man page Source code
pachterlab/sleuth documentation built on June 30, 2018, 1:14 p.m.