Release notes
1.2.0
Bug fixes
Removed
python <3.10
limitation.Forced
np.float32
type to output ofget_contrast
.Made
summarize_acts
compatible with older versions of numpy.extract_psbulk_inputs
now checks if mat and obs have matching indexes.plot_volcano
now correctly can plot networks with different source names.
Changes
extract
now removes empty samples and features.run_consensus
now follows the same format as other methods, old function is now calledcons
.get_pseudobulk
now checks if input are raw integer counts.plot_volcano
now can plot without subsetting features by a network and can save plots to disk.plot_volcano
now usesadjustText
to better plot text labels.plot_volcano
now can set logFCs and p-value limits for outliers.get_top_targets
now can also work without subsetting features by a network and returns significant adjusted p-values.get_contrast
now can also work without needing to group.udt
andmdt
now check ifskranger
andsklearn
are installed, respectively.get_toy_data
now contains more example TFs.get_top_targets
now returnslogFCs
andpvals
as column names instead oflogFC
andpval
.format_contrast_results
now returns also the adjusted p-value.
Additions
Added
dense_run
util function which runs methods ignoring zeros in the data.Added
plot_violins
andplot_barplot
functions.Added
p_adjust_fdr
util function to correct p-values for FDR.Added
get_ora_df
function to infer ora from lists of genes instead of an input mat.Added
shuffle_net
function to randomize networks.Added benchmarking metrics
metric_auroc
,metric_auprc
,metric_mcauroc
andmetric_mcauprc
.Added
get_toy_benchmark_data
function to generate a toy example for benchmarking.Added
show_metrics
function to show available metrics.Added
benchmark
,format_benchmark_inputs
andget_performances
functions to benchmark methods and nets.Added
plot_metrics_scatter
function to plot the results of running the benchmarking pipeline.Added
plot_metrics_scatter_cols
function to plot the results of running the benchmarking pipeline grouped by two levels.Added
plot_metrics_scatter
function to plot the results of running the benchmarking pipeline.Added
plot_metrics_boxplot
function to plot the distributions of Monte-Carlo benchmarking metrics.
1.1.0
Bug fixes
Fixed
get_pseudobulk
errors.Fixed
get_progeny
to correctly return non duplicate entries.Fixed
run_viper
parallelization error.Fixed
run_ora
to correctly deal with random ties.
Changes
get_dorothea
now returns an ordered dataframe.get_contrast
now prints warnings instead of returning an empty dataframe.
Additions
Added
get_top_targets
util function.Added
format_contrast_results
util function.