ngs_toolkit
0.19.2
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ngs_toolkit
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C
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D
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Z
A
all_to_igv() (in module ngs_toolkit.cnv)
Analysis (class in ngs_toolkit.analysis)
annotate_features() (ngs_toolkit.analysis.Analysis method)
annotate_matrix() (ngs_toolkit.analysis.Analysis method)
annotate_samples() (ngs_toolkit.analysis.Analysis method)
annotate_with_chrom_bands() (ngs_toolkit.cnv.CNVAnalysis method)
assess_cell_cycle() (in module ngs_toolkit.rnaseq)
ATACSeqAnalysis (class in ngs_toolkit.atacseq)
B
barmap() (in module ngs_toolkit.graphics)
bed_to_fasta() (in module ngs_toolkit.utils)
bed_to_fasta_through_2bit() (in module ngs_toolkit.utils)
bed_to_fasta_through_fasta() (in module ngs_toolkit.utils)
bed_to_index() (in module ngs_toolkit.utils)
bedtool_to_index() (in module ngs_toolkit.utils)
C
calculate_peak_support() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
(ngs_toolkit.chipseq.ChIPSeqAnalysis method)
call_peaks_from_comparisons() (ngs_toolkit.chipseq.ChIPSeqAnalysis method)
characterize_regions_function() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
ChIPSeqAnalysis (class in ngs_toolkit.chipseq)
chunks() (in module ngs_toolkit.utils)
CNVAnalysis (class in ngs_toolkit.cnv)
collect_bitseq_output() (ngs_toolkit.rnaseq.RNASeqAnalysis method)
collect_coverage() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
collect_differential_analysis() (ngs_toolkit.analysis.Analysis method)
collect_differential_enrichment() (ngs_toolkit.analysis.Analysis method)
collect_esat_output() (ngs_toolkit.rnaseq.RNASeqAnalysis method)
collect_md5_sums() (in module ngs_toolkit.utils)
compress_file() (in module ngs_toolkit.utils)
count_bam_file_length() (in module ngs_toolkit.utils)
count_dataframe_values() (in module ngs_toolkit.utils)
count_lines() (in module ngs_toolkit.utils)
count_reads_in_intervals() (in module ngs_toolkit.utils)
cqn() (in module ngs_toolkit.utils)
D
decompress_file() (in module ngs_toolkit.utils)
deseq_analysis() (in module ngs_toolkit.general)
deseq_results_to_bed_file() (in module ngs_toolkit.utils)
differential_analysis() (ngs_toolkit.analysis.Analysis method)
differential_enrichment() (ngs_toolkit.analysis.Analysis method)
differential_from_bivariate_fit() (in module ngs_toolkit.general)
differential_overlap() (ngs_toolkit.analysis.Analysis method)
download_file() (in module ngs_toolkit.utils)
download_gzip_file() (in module ngs_toolkit.utils)
E
enrichr() (in module ngs_toolkit.general)
F
filter_peaks() (ngs_toolkit.chipseq.ChIPSeqAnalysis method)
fix_batch_effect_limma() (in module ngs_toolkit.general)
from_pep() (ngs_toolkit.analysis.Analysis method)
from_pickle() (ngs_toolkit.analysis.Analysis method)
G
generate_bam_file() (in module ngs_toolkit.demo.data_generator)
generate_count_matrix() (in module ngs_toolkit.demo.data_generator)
generate_data() (in module ngs_toolkit.demo.data_generator)
generate_peak_file() (in module ngs_toolkit.demo.data_generator)
generate_project() (in module ngs_toolkit.demo.data_generator)
generate_projects() (in module ngs_toolkit.demo.data_generator)
generate_report() (ngs_toolkit.analysis.Analysis method)
generate_sample_input_files() (in module ngs_toolkit.demo.data_generator)
get_blacklist_annotations() (in module ngs_toolkit.general)
get_cnv_data() (ngs_toolkit.cnv.CNVAnalysis method)
get_consensus_sites() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
(ngs_toolkit.chipseq.ChIPSeqAnalysis method)
get_gene_expression() (ngs_toolkit.rnaseq.RNASeqAnalysis method)
get_gene_level_changes() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
get_gene_level_matrix() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
get_genome_reference() (in module ngs_toolkit.general)
get_genomic_bins() (in module ngs_toolkit.demo.data_generator)
get_genomic_context() (in module ngs_toolkit.general)
get_level_colors() (ngs_toolkit.analysis.Analysis method)
get_matrix() (ngs_toolkit.analysis.Analysis method)
get_matrix_stats() (ngs_toolkit.analysis.Analysis method)
get_peak_chromatin_state() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
get_peak_gccontent_length() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
get_peak_gene_annotation() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
get_peak_genomic_location() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
get_random_genes() (in module ngs_toolkit.demo.data_generator)
get_random_genomic_locations() (in module ngs_toolkit.demo.data_generator)
get_region_lengths() (in module ngs_toolkit.utils)
get_regions_per_chromosomes() (in module ngs_toolkit.utils)
get_resources() (ngs_toolkit.analysis.Analysis method)
get_sample_annotation() (ngs_toolkit.analysis.Analysis method)
get_sex_chrom_ratio() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
get_supported_peaks() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
(ngs_toolkit.chipseq.ChIPSeqAnalysis method)
get_this_file_or_timestamped() (in module ngs_toolkit.utils)
get_timestamp() (in module ngs_toolkit.utils)
get_total_region_area() (in module ngs_toolkit.utils)
get_tss_annotations() (in module ngs_toolkit.general)
H
have_unbuffered_output() (in module ngs_toolkit.utils)
homer_call_chipseq_peak_job() (in module ngs_toolkit.utils)
homer_combine_motifs() (in module ngs_toolkit.general)
homer_peaks_to_bed() (in module ngs_toolkit.utils)
I
initialize_analysis_of_data_type() (in module ngs_toolkit.demo.data_generator)
is_analysis_descendent() (in module ngs_toolkit.utils)
is_running_inside_ipython() (in module ngs_toolkit.utils)
K
knockout_plot() (in module ngs_toolkit.rnaseq)
L
least_squares_fit() (in module ngs_toolkit.general)
load_data() (ngs_toolkit.analysis.Analysis method)
(ngs_toolkit.atacseq.ATACSeqAnalysis method)
(ngs_toolkit.cnv.CNVAnalysis method)
location_index_to_bed() (in module ngs_toolkit.utils)
log_pvalues() (in module ngs_toolkit.utils)
logit() (in module ngs_toolkit.utils)
lola() (in module ngs_toolkit.general)
M
macs2_call_chipseq_peak() (in module ngs_toolkit.utils)
measure_coverage() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
N
ngs_toolkit (module)
ngs_toolkit.analysis (module)
ngs_toolkit.atacseq (module)
ngs_toolkit.chipseq (module)
ngs_toolkit.cnv (module)
ngs_toolkit.demo.data_generator (module)
ngs_toolkit.general (module)
ngs_toolkit.graphics (module)
ngs_toolkit.parsers (module)
ngs_toolkit.rnaseq (module)
ngs_toolkit.utils (module)
normalize() (ngs_toolkit.analysis.Analysis method)
(ngs_toolkit.cnv.CNVAnalysis method)
normalize_by_background() (ngs_toolkit.chipseq.ChIPSeqAnalysis method)
normalize_cqn() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
normalize_median() (ngs_toolkit.analysis.Analysis method)
normalize_pca() (ngs_toolkit.analysis.Analysis method)
normalize_quantiles() (ngs_toolkit.analysis.Analysis method)
normalize_quantiles_p() (in module ngs_toolkit.utils)
normalize_quantiles_r() (in module ngs_toolkit.utils)
normalize_rpm() (ngs_toolkit.analysis.Analysis method)
normalize_vst() (ngs_toolkit.analysis.Analysis method)
P
parse_ame() (in module ngs_toolkit.parsers)
parse_great_enrichment() (in module ngs_toolkit.parsers)
parse_homer() (in module ngs_toolkit.parsers)
plot_all_data() (ngs_toolkit.cnv.CNVAnalysis method)
plot_comparison_correlations() (in module ngs_toolkit.graphics)
plot_differential() (ngs_toolkit.analysis.Analysis method)
plot_differential_enrichment() (ngs_toolkit.analysis.Analysis method)
plot_expression_characteristics() (ngs_toolkit.rnaseq.RNASeqAnalysis method)
plot_peak_characteristics() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
plot_projection() (in module ngs_toolkit.graphics)
plot_raw_coverage() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
plot_region_context_enrichment() (in module ngs_toolkit.graphics)
plot_segmentation_stats() (ngs_toolkit.cnv.CNVAnalysis method)
plot_stats_per_chromosome() (ngs_toolkit.cnv.CNVAnalysis method)
project_to_geo() (in module ngs_toolkit.general)
Q
query_biomart() (in module ngs_toolkit.general)
R
r2pandas_df() (in module ngs_toolkit.utils)
radar_plot() (in module ngs_toolkit.graphics)
read_bed_file_three_columns() (in module ngs_toolkit.utils)
recarray2pandas_df() (in module ngs_toolkit.utils)
record_analysis_output() (in module ngs_toolkit.utils)
record_output_file() (ngs_toolkit.analysis.Analysis method)
region_context_enrichment() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
remove_factor_from_matrix() (ngs_toolkit.analysis.Analysis method)
remove_timestamp_if_existing() (in module ngs_toolkit.utils)
rename_sample_files() (in module ngs_toolkit.general)
RNASeqAnalysis (class in ngs_toolkit.rnaseq)
run_enrichment_jobs() (in module ngs_toolkit.general)
run_full_analysis_recipe() (ngs_toolkit.analysis.Analysis method)
S
segment_genome() (ngs_toolkit.cnv.CNVAnalysis method)
set_consensus_sites() (ngs_toolkit.atacseq.ATACSeqAnalysis method)
set_matrix() (ngs_toolkit.analysis.Analysis method)
set_organism_genome() (ngs_toolkit.analysis.Analysis method)
set_project_attributes() (ngs_toolkit.analysis.Analysis method)
set_samples_input_files() (ngs_toolkit.analysis.Analysis method)
setup_config() (in module ngs_toolkit)
setup_graphic_preferences() (in module ngs_toolkit)
setup_logger() (in module ngs_toolkit)
signed_max() (in module ngs_toolkit.utils)
sort_bed_nicely() (in module ngs_toolkit.utils)
sorted_nicely() (in module ngs_toolkit.utils)
standard_score() (in module ngs_toolkit.utils)
submit_job() (in module ngs_toolkit.utils)
subtract_principal_component() (in module ngs_toolkit.general)
subtract_principal_component_by_attribute() (in module ngs_toolkit.general)
summarize_peaks_from_comparisons() (ngs_toolkit.chipseq.ChIPSeqAnalysis method)
T
timedelta_to_years() (in module ngs_toolkit.utils)
to_bed_index() (in module ngs_toolkit.utils)
to_igv() (in module ngs_toolkit.cnv)
to_pickle() (ngs_toolkit.analysis.Analysis method)
U
unsupervised_analysis() (ngs_toolkit.analysis.Analysis method)
update() (ngs_toolkit.analysis.Analysis method)
Z
z_score() (in module ngs_toolkit.utils)
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