Getting Started
is_proteodata
check_proteodata
protein_id
peptide_id
sample_id
pr.read.long()
.uns
API reference
proteopy
.read
.diann
diann()
.long
long()
.ann
.var
var()
.samples
samples()
.proteins_from_csv
proteins_from_csv()
.pp
.filter_samples
filter_samples()
.filter_samples_completeness
filter_samples_completeness()
.filter_var
filter_var()
.filter_var_completeness
filter_var_completeness()
.filter_proteins_by_peptide_count
filter_proteins_by_peptide_count()
.filter_samples_by_category_count
filter_samples_by_category_count()
.remove_zero_variance_vars
remove_zero_variance_vars()
.remove_contaminants
remove_contaminants()
.normalize_median
normalize_median()
.impute_downshift
impute_downshift()
.extract_peptide_groups
extract_peptide_groups()
.summarize_modifications
summarize_modifications()
.summarize_overlapping_peptides
summarize_overlapping_peptides()
.quantify_proteins
quantify_proteins()
.quantify_proteoforms
quantify_proteoforms()
.calculate_cv
calculate_cv()
.tl
.differential_abundance
differential_abundance()
.hclustv_tree
hclustv_tree()
.hclustv_cluster_ann
hclustv_cluster_ann()
.hclustv_profiles
hclustv_profiles()
.pairwise_peptide_correlations
pairwise_peptide_correlations()
.peptide_dendograms_by_correlation
peptide_dendograms_by_correlation()
.peptide_clusters_from_dendograms
peptide_clusters_from_dendograms()
.proteoform_scores
proteoform_scores()
.pl
.peptide_intensities
peptide_intensities()
.proteoform_intensities
proteoform_intensities()
.intensity_hist
intensity_hist()
.intensity_box_per_sample
intensity_box_per_sample()
.box
box()
.abundance_rank
abundance_rank()
.binary_heatmap
binary_heatmap()
.completeness
completeness()
.completeness_per_sample
completeness_per_sample()
.completeness_per_var
completeness_per_var()
.n_samples_per_category
n_samples_per_category()
.n_peptides_per_sample
n_peptides_per_sample()
.n_proteins_per_sample
n_proteins_per_sample()
.n_cat1_per_cat2_hist
n_cat1_per_cat2_hist()
.n_peptides_per_protein
n_peptides_per_protein()
.n_proteoforms_per_protein
n_proteoforms_per_protein()
.cv_by_group
cv_by_group()
.sample_correlation_matrix
sample_correlation_matrix()
.volcano_plot
volcano_plot()
.differential_abundance_box
differential_abundance_box()
.hclustv_profiles_heatmap
hclustv_profiles_heatmap()
.hclustv_silhouette
hclustv_silhouette()
.hclustv_elbow
hclustv_elbow()
.hclustv_profile_intensities
hclustv_profile_intensities()
.get
.proteoforms_df
proteoforms_df()
.differential_abundance_df
differential_abundance_df()
.tests
tests()
.datasets
.karayel_2020
karayel_2020()
.download
.contaminants
contaminants()
.utils
.is_proteodata
is_proteodata()
.check_proteodata
check_proteodata()
.is_log_transformed
is_log_transformed()
About
These tutorials demonstrate how to use ProteoPy for common proteomics analysis workflows.