Release notes
1.3.4
Changes
get_pseudobulk
now has new arguments:mode
to change how to summarize profiles andskip_checks
to bypass checks.OmniPath functions now accept more organism synonyms.
Bug fixes
Fixed empty text labels bug for
adjustText==0.8
.
1.3.3
Bug fixes
read_gmt
is now properly exported.
1.3.2
Bug fixes
plot_metrics_scatter_cols
now deals with missing sources when comparing nets.
Changes
get_pseudobulk
andget_acts
now have adtype
argument due to futureAnnData
changes.plot_metrics_scatter
andplot_metrics_boxplot
now useGroupBy.mean(numeric_only=True)
.
Additions
Added
swap_layer
function to easily moveadata
layers to.X
.Added
read_gmt
function to read GMT files containing gene sets.
1.3.1
Changes
Omnipath wrappers (
get_resource
,get_dorothea
andget_progeny
) now accept any organism name.
1.3.0
Bug fixes
Fixed change in api from
sklearn.tree
.Forced gene names in
extract
to be inunicode
format.Changed integer format from
int32
toint64
to accommodate larger datasets across methods.
Additions
Added conversion utility function
translate_net
to translate nets across organisms.
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.