AUTHORS.rst
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
RNAlysis.egg-info/PKG-INFO
RNAlysis.egg-info/SOURCES.txt
RNAlysis.egg-info/dependency_links.txt
RNAlysis.egg-info/not-zip-safe
RNAlysis.egg-info/requires.txt
RNAlysis.egg-info/top_level.txt
docs/index.rst
docs/make.bat
docs/build/_images/bigtable_en.png
docs/build/_images/clustergram.png
docs/build/_images/enrichment_randomization.png
docs/build/_images/go_en.png
docs/build/_images/pairplot.png
docs/build/_images/pca.png
docs/build/_images/plot_expression.png
docs/build/_images/rpm_vs_rpm.png
docs/build/_images/tissue_en.png
docs/build/_images/upsetplot.png
docs/build/_images/venn.png
docs/build/_images/violin.png
docs/build/_images/volcano.png
docs/build/_static/file.png
docs/build/_static/minus.png
docs/build/_static/plus.png
docs/source/authors.rst
docs/source/clustergram.png
docs/source/conf.py
docs/source/contributing.rst
docs/source/enrichment_randomization.png
docs/source/go_en.png
docs/source/history.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/pairplot.png
docs/source/pca.png
docs/source/phenotype_en.png
docs/source/plot_expression.png
docs/source/readme.rst
docs/source/rnalysis.enrichment.FeatureSet.__init__.rst
docs/source/rnalysis.enrichment.FeatureSet.biotypes.rst
docs/source/rnalysis.enrichment.FeatureSet.difference.rst
docs/source/rnalysis.enrichment.FeatureSet.enrich_randomization.rst
docs/source/rnalysis.enrichment.FeatureSet.enrich_randomization_parallel.rst
docs/source/rnalysis.enrichment.FeatureSet.go_enrichment.rst
docs/source/rnalysis.enrichment.FeatureSet.intersection.rst
docs/source/rnalysis.enrichment.FeatureSet.rst
docs/source/rnalysis.enrichment.FeatureSet.save_txt.rst
docs/source/rnalysis.enrichment.FeatureSet.symmetric_difference.rst
docs/source/rnalysis.enrichment.FeatureSet.union.rst
docs/source/rnalysis.enrichment.rst
docs/source/rnalysis.enrichment.upset_plot.rst
docs/source/rnalysis.enrichment.venn_diagram.rst
docs/source/rnalysis.filtering.CountFilter.__init__.rst
docs/source/rnalysis.filtering.CountFilter.biotypes.rst
docs/source/rnalysis.filtering.CountFilter.clustergram.rst
docs/source/rnalysis.filtering.CountFilter.describe.rst
docs/source/rnalysis.filtering.CountFilter.difference.rst
docs/source/rnalysis.filtering.CountFilter.filter_biotype.rst
docs/source/rnalysis.filtering.CountFilter.filter_by_attribute.rst
docs/source/rnalysis.filtering.CountFilter.filter_by_row_sum.rst
docs/source/rnalysis.filtering.CountFilter.filter_low_reads.rst
docs/source/rnalysis.filtering.CountFilter.filter_percentile.rst
docs/source/rnalysis.filtering.CountFilter.filter_top_n.rst
docs/source/rnalysis.filtering.CountFilter.fold_change.rst
docs/source/rnalysis.filtering.CountFilter.from_folder.rst
docs/source/rnalysis.filtering.CountFilter.head.rst
docs/source/rnalysis.filtering.CountFilter.intersection.rst
docs/source/rnalysis.filtering.CountFilter.normalize_to_rpm.rst
docs/source/rnalysis.filtering.CountFilter.normalize_with_scaling_factors.rst
docs/source/rnalysis.filtering.CountFilter.number_filters.rst
docs/source/rnalysis.filtering.CountFilter.pairplot.rst
docs/source/rnalysis.filtering.CountFilter.pca.rst
docs/source/rnalysis.filtering.CountFilter.plot_expression.rst
docs/source/rnalysis.filtering.CountFilter.print_features.rst
docs/source/rnalysis.filtering.CountFilter.rst
docs/source/rnalysis.filtering.CountFilter.save_csv.rst
docs/source/rnalysis.filtering.CountFilter.scatter_sample_vs_sample.rst
docs/source/rnalysis.filtering.CountFilter.split_by_attribute.rst
docs/source/rnalysis.filtering.CountFilter.split_by_percentile.rst
docs/source/rnalysis.filtering.CountFilter.split_by_reads.rst
docs/source/rnalysis.filtering.CountFilter.symmetric_difference.rst
docs/source/rnalysis.filtering.CountFilter.tail.rst
docs/source/rnalysis.filtering.CountFilter.text_filters.rst
docs/source/rnalysis.filtering.CountFilter.union.rst
docs/source/rnalysis.filtering.CountFilter.violin_plot.rst
docs/source/rnalysis.filtering.DESeqFilter.__init__.rst
docs/source/rnalysis.filtering.DESeqFilter.biotypes.rst
docs/source/rnalysis.filtering.DESeqFilter.describe.rst
docs/source/rnalysis.filtering.DESeqFilter.difference.rst
docs/source/rnalysis.filtering.DESeqFilter.filter_abs_log2_fold_change.rst
docs/source/rnalysis.filtering.DESeqFilter.filter_biotype.rst
docs/source/rnalysis.filtering.DESeqFilter.filter_by_attribute.rst
docs/source/rnalysis.filtering.DESeqFilter.filter_fold_change_direction.rst
docs/source/rnalysis.filtering.DESeqFilter.filter_percentile.rst
docs/source/rnalysis.filtering.DESeqFilter.filter_significant.rst
docs/source/rnalysis.filtering.DESeqFilter.filter_top_n.rst
docs/source/rnalysis.filtering.DESeqFilter.head.rst
docs/source/rnalysis.filtering.DESeqFilter.intersection.rst
docs/source/rnalysis.filtering.DESeqFilter.number_filters.rst
docs/source/rnalysis.filtering.DESeqFilter.print_features.rst
docs/source/rnalysis.filtering.DESeqFilter.rst
docs/source/rnalysis.filtering.DESeqFilter.save_csv.rst
docs/source/rnalysis.filtering.DESeqFilter.split_by_attribute.rst
docs/source/rnalysis.filtering.DESeqFilter.split_by_percentile.rst
docs/source/rnalysis.filtering.DESeqFilter.split_fold_change_direction.rst
docs/source/rnalysis.filtering.DESeqFilter.symmetric_difference.rst
docs/source/rnalysis.filtering.DESeqFilter.tail.rst
docs/source/rnalysis.filtering.DESeqFilter.text_filters.rst
docs/source/rnalysis.filtering.DESeqFilter.union.rst
docs/source/rnalysis.filtering.DESeqFilter.volcano_plot.rst
docs/source/rnalysis.filtering.Filter.__init__.rst
docs/source/rnalysis.filtering.Filter.biotypes.rst
docs/source/rnalysis.filtering.Filter.describe.rst
docs/source/rnalysis.filtering.Filter.difference.rst
docs/source/rnalysis.filtering.Filter.filter_biotype.rst
docs/source/rnalysis.filtering.Filter.filter_by_attribute.rst
docs/source/rnalysis.filtering.Filter.filter_percentile.rst
docs/source/rnalysis.filtering.Filter.filter_top_n.rst
docs/source/rnalysis.filtering.Filter.head.rst
docs/source/rnalysis.filtering.Filter.intersection.rst
docs/source/rnalysis.filtering.Filter.number_filters.rst
docs/source/rnalysis.filtering.Filter.print_features.rst
docs/source/rnalysis.filtering.Filter.rst
docs/source/rnalysis.filtering.Filter.save_csv.rst
docs/source/rnalysis.filtering.Filter.split_by_attribute.rst
docs/source/rnalysis.filtering.Filter.split_by_percentile.rst
docs/source/rnalysis.filtering.Filter.symmetric_difference.rst
docs/source/rnalysis.filtering.Filter.tail.rst
docs/source/rnalysis.filtering.Filter.text_filters.rst
docs/source/rnalysis.filtering.Filter.union.rst
docs/source/rnalysis.filtering.FoldChangeFilter.__init__.rst
docs/source/rnalysis.filtering.FoldChangeFilter.biotypes.rst
docs/source/rnalysis.filtering.FoldChangeFilter.describe.rst
docs/source/rnalysis.filtering.FoldChangeFilter.difference.rst
docs/source/rnalysis.filtering.FoldChangeFilter.filter_abs_log2_fold_change.rst
docs/source/rnalysis.filtering.FoldChangeFilter.filter_biotype.rst
docs/source/rnalysis.filtering.FoldChangeFilter.filter_by_attribute.rst
docs/source/rnalysis.filtering.FoldChangeFilter.filter_fold_change_direction.rst
docs/source/rnalysis.filtering.FoldChangeFilter.filter_percentile.rst
docs/source/rnalysis.filtering.FoldChangeFilter.filter_top_n.rst
docs/source/rnalysis.filtering.FoldChangeFilter.head.rst
docs/source/rnalysis.filtering.FoldChangeFilter.intersection.rst
docs/source/rnalysis.filtering.FoldChangeFilter.number_filters.rst
docs/source/rnalysis.filtering.FoldChangeFilter.print_features.rst
docs/source/rnalysis.filtering.FoldChangeFilter.randomization_test.rst
docs/source/rnalysis.filtering.FoldChangeFilter.rst
docs/source/rnalysis.filtering.FoldChangeFilter.save_csv.rst
docs/source/rnalysis.filtering.FoldChangeFilter.split_by_attribute.rst
docs/source/rnalysis.filtering.FoldChangeFilter.split_by_percentile.rst
docs/source/rnalysis.filtering.FoldChangeFilter.split_fold_change_direction.rst
docs/source/rnalysis.filtering.FoldChangeFilter.symmetric_difference.rst
docs/source/rnalysis.filtering.FoldChangeFilter.tail.rst
docs/source/rnalysis.filtering.FoldChangeFilter.text_filters.rst
docs/source/rnalysis.filtering.FoldChangeFilter.union.rst
docs/source/rnalysis.filtering.rst
docs/source/rnalysis.general.load_csv.rst
docs/source/rnalysis.general.parse_gene_name_string.rst
docs/source/rnalysis.general.parse_sequence_name_string.rst
docs/source/rnalysis.general.parse_wbgene_string.rst
docs/source/rnalysis.general.read_attr_ref_table_path.rst
docs/source/rnalysis.general.read_biotype_ref_table_path.rst
docs/source/rnalysis.general.rst
docs/source/rnalysis.general.save_to_csv.rst
docs/source/rnalysis.general.set_attr_ref_table_path.rst
docs/source/rnalysis.general.set_biotype_ref_table_path.rst
docs/source/rnalysis.general.start_parallel_session.rst
docs/source/rnalysis.rst
docs/source/rpm_vs_rpm.png
docs/source/tissue_en.png
docs/source/upsetplot.png
docs/source/user_guide.rst
docs/source/venn.png
docs/source/violin.png
docs/source/volcano.png
rnalysis/__init__.py
rnalysis/enrichment.py
rnalysis/filtering.py
rnalysis/general.py
tests/__init__.py
tests/attr_ref_table_for_examples.csv
tests/attr_ref_table_for_tests.csv
tests/attr_ref_table_for_tests_biotype.csv
tests/attr_ref_table_for_tests_specified_bg.csv
tests/biotype_ref_table_for_tests.csv
tests/biotypes_truth.csv
tests/counted.csv
tests/counted_above60_rpm.csv
tests/counted_below60_rpm.csv
tests/counted_biotype.csv
tests/counted_biotype_no_piRNA.csv
tests/counted_biotype_piRNA.csv
tests/counted_biotype_piRNA_protein_coding.csv
tests/counted_biotype_piRNA_protein_coding_opposite.csv
tests/counted_biotype_protein_coding.csv
tests/counted_eq.csv
tests/counted_filter_by_bigtable.csv
tests/counted_filter_by_bigtable_intersect_truth.csv
tests/counted_filter_by_bigtable_union_truth.csv
tests/counted_fold_change.csv
tests/counted_fold_change_truth.csv
tests/counted_low_rpm.csv
tests/counted_low_rpm_truth.csv
tests/counted_missing_rows.csv
tests/counted_missing_rows_deleted.csv
tests/counted_sorted_multiple_truth.csv
tests/enrichment_randomization_res.csv
tests/fc_1.csv
tests/fc_2.csv
tests/fc_randomization_truth.csv
tests/fcfilter_abs_fold_change_truth.csv
tests/pytest.ini
tests/sample_deseq.csv
tests/scaling_factors.csv
tests/test_bg_genes_from_filter_object.csv
tests/test_count_from_folder_all_expr.csv
tests/test_count_from_folder_all_feature.csv
tests/test_count_from_folder_norm.csv
tests/test_deseq.csv
tests/test_deseq_biotype.csv
tests/test_deseq_biotype_piRNA.csv
tests/test_deseq_biotype_piRNA_opposite.csv
tests/test_deseq_biotype_piRNA_protein_coding.csv
tests/test_deseq_biotype_piRNA_protein_coding_opposite.csv
tests/test_deseq_biotype_protein_coding.csv
tests/test_deseq_bottom10_text_descend.csv
tests/test_deseq_bottom7.csv
tests/test_deseq_fc.csv
tests/test_deseq_fc_4_truth.csv
tests/test_deseq_fc_neg_truth.csv
tests/test_deseq_fc_pos_truth.csv
tests/test_deseq_gt.csv
tests/test_deseq_lt.csv
tests/test_deseq_no_nans.csv
tests/test_deseq_not_sig_truth.csv
tests/test_deseq_percentile.csv
tests/test_deseq_percentile_0.25.csv
tests/test_deseq_percentile_0.75.csv
tests/test_deseq_set_ops_1.csv
tests/test_deseq_set_ops_1_inplace_difference.csv
tests/test_deseq_set_ops_1_inplace_intersection.csv
tests/test_deseq_set_ops_2.csv
tests/test_deseq_set_ops_2_inplace_difference.csv
tests/test_deseq_set_ops_2_inplace_intersection.csv
tests/test_deseq_sig.csv
tests/test_deseq_sig_truth.csv
tests/test_deseq_textcol.csv
tests/test_deseq_top10.csv
tests/test_deseq_top10_text_ascend.csv
tests/test_deseq_with_nan.csv
tests/test_deseq_with_nan_sorted_nanfirst_truth.csv
tests/test_deseq_with_nan_sorted_nanlast_truth.csv
tests/test_enrichment.py
tests/test_filter_row_sum.csv
tests/test_filtering.py
tests/test_general.py
tests/test_load_csv.csv
tests/test_norm_reads_rpm.csv
tests/test_norm_scaling_factors.csv
tests/text_filters.csv
tests/text_filters_ct.csv
tests/text_filters_eq.csv
tests/text_filters_ew.csv
tests/text_filters_sw.csv
tests/tox.ini
tests/uncounted.csv
tests/.pytest_cache/.gitignore
tests/.pytest_cache/CACHEDIR.TAG
tests/.pytest_cache/README.md
tests/.pytest_cache/v/cache/lastfailed
tests/.pytest_cache/v/cache/nodeids
tests/.pytest_cache/v/cache/stepwise
tests/test_count_from_folder/file1.txt
tests/test_count_from_folder/file2.txt