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riboraptor 0.3.0 documentation
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Contents
Installation
Example Workflow
Manual
API Usage
Scores
riboraptor
History
Contributing
Credits
Docs
Index
Index
B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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W
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Y
B
bam_to_bedgraph() (in module riboraptor.count)
bedgraph_to_bigwig() (in module riboraptor.count)
bwshift() (in module riboraptor.helpers)
bwsum() (in module riboraptor.helpers)
C
calculate_cdf() (in module riboraptor.statistics)
check_file_exists() (in module riboraptor.helpers)
chromosomes (riboraptor.fasta.FastaReader attribute)
(riboraptor.wig.WigReader attribute)
close() (riboraptor.hdf_parser.HDFParser method)
(riboraptor.sradb.SRAdb method)
(riboraptor.wig.WigReader method)
codon_to_anticodon() (in module riboraptor.helpers)
coherence() (in module riboraptor.coherence)
coherence_ft() (in module riboraptor.coherence)
coherence_pvalue() (in module riboraptor.statistics)
complement() (riboraptor.fasta.FastaReader method)
complementary_strand() (in module riboraptor.helpers)
convert_gse_to_srp() (riboraptor.sradb.SRAdb method)
copy_sra_data() (in module riboraptor.utils)
count_uniq_mapping_reads() (in module riboraptor.count)
counts_to_tpm() (in module riboraptor.helpers)
create_bam_index() (in module riboraptor.helpers)
create_config_file() (in module riboraptor.utils)
create_ideal_periodic_signal() (in module riboraptor.helpers)
create_metagene_from_multi_bigwig() (in module riboraptor.hdf_parser)
create_trackdb() (in module riboraptor.tracks)
create_wavelet() (in module riboraptor.plotting)
D
desc_table() (riboraptor.sradb.SRAdb method)
deseq2_normalization() (in module riboraptor.normalization)
determine_cell_type() (in module riboraptor.utils)
dtw() (in module riboraptor.dtw)
E
export_gene_coverages() (in module riboraptor.count)
export_gene_sequences() (in module riboraptor.sequence)
export_metagene_coverage() (in module riboraptor.count)
export_read_counts() (in module riboraptor.count)
export_read_length() (in module riboraptor.count)
extract_uniq_mapping_reads() (in module riboraptor.count)
F
FastaReader (class in riboraptor.fasta)
fastq_kmer_histogram() (in module riboraptor.kmer)
featurecounts_to_tpm() (in module riboraptor.helpers)
filter_single_end_samples() (in module riboraptor.utils)
find_first_non_none() (in module riboraptor.helpers)
find_last_non_none() (in module riboraptor.helpers)
func() (in module riboraptor.parallel)
G
gene_coverage() (in module riboraptor.count)
gene_sequence() (in module riboraptor.sequence)
get_bam_coverage() (in module riboraptor.count)
get_bam_coverage_on_bed() (in module riboraptor.count)
get_bigwigtrack_text() (in module riboraptor.tracks)
get_cell_line_or_tissue() (in module riboraptor.utils)
get_compositetrack_text() (in module riboraptor.tracks)
get_coverage() (riboraptor.hdf_parser.HDFParser method)
get_enrichment_cds_stats() (in module riboraptor.utils)
get_fragment_enrichment_score() (in module riboraptor.utils)
get_multiwigtrack_text() (in module riboraptor.tracks)
get_path() (in module riboraptor.dtw)
get_periodicity() (in module riboraptor.coherence)
get_query() (riboraptor.sradb.SRAdb method)
get_query_alignment_length_dist() (riboraptor.hdf_parser.HDFParser method)
get_read_length_dist() (riboraptor.hdf_parser.HDFParser method)
get_region_sizes() (in module riboraptor.count)
(in module riboraptor.helpers)
get_row_count() (riboraptor.sradb.SRAdb method)
get_strain_type() (in module riboraptor.utils)
get_strandedness() (in module riboraptor.helpers)
get_supertrack_text() (in module riboraptor.tracks)
get_table_counts() (riboraptor.sradb.SRAdb method)
get_tissue_type() (in module riboraptor.utils)
H
hdf_to_bigwig() (in module riboraptor.hdf_parser)
HDFParser (class in riboraptor.hdf_parser)
htseq_to_tpm() (in module riboraptor.helpers)
I
identify_peaks() (in module riboraptor.helpers)
infer_protocol() (in module riboraptor.infer_protocol)
Interval (class in riboraptor.interval)
is_read_uniq_mapping() (in module riboraptor.helpers)
K
KDE() (in module riboraptor.statistics)
KS_test() (in module riboraptor.statistics)
L
list_fields() (riboraptor.sradb.SRAdb method)
list_tables() (riboraptor.sradb.SRAdb method)
list_to_ranges() (in module riboraptor.helpers)
load_pickle() (in module riboraptor.helpers)
load_tpm() (in module riboraptor.utils)
M
mapping_reads_summary() (in module riboraptor.count)
merge_bigwigs() (in module riboraptor.hdf_parser)
merge_gene_coverages() (in module riboraptor.count)
merge_intervals() (in module riboraptor.helpers)
merge_read_counts() (in module riboraptor.count)
millify() (in module riboraptor.helpers)
mkdir_p() (in module riboraptor.helpers)
N
naive_periodicity() (in module riboraptor.coherence)
normalize_bw_hdf() (in module riboraptor.hdf_parser)
O
open() (riboraptor.sradb.SRAdb method)
order_dataframe() (in module riboraptor.helpers)
OrderedCounter (class in riboraptor.count)
P
pad_five_prime_or_truncate() (in module riboraptor.helpers)
pad_or_truncate() (in module riboraptor.helpers)
ParallelExecutor() (in module riboraptor.parallel)
parse_star_logs() (in module riboraptor.helpers)
path_leaf() (in module riboraptor.helpers)
plot_featurewise_barplot() (in module riboraptor.plotting)
plot_framewise_counts() (in module riboraptor.plotting)
plot_periodicity_df() (in module riboraptor.plotting)
plot_read_counts() (in module riboraptor.plotting)
plot_read_length_dist() (in module riboraptor.plotting)
plot_warped_timeseries() (in module riboraptor.dtw)
Q
query() (riboraptor.fasta.FastaReader method)
(riboraptor.wig.WigReader method)
R
r2() (in module riboraptor.helpers)
read_bed_as_intervaltree() (in module riboraptor.helpers)
read_chrom_sizes() (in module riboraptor.helpers)
read_enrichment() (in module riboraptor.count)
(in module riboraptor.helpers)
read_htseq() (in module riboraptor.helpers)
read_refseq_bed() (in module riboraptor.helpers)
reverse_complement() (riboraptor.fasta.FastaReader method)
riboraptor (module)
riboraptor.cli (module)
riboraptor.coherence (module)
riboraptor.count (module)
riboraptor.download (module)
riboraptor.dtw (module)
riboraptor.fasta (module)
riboraptor.genome (module)
riboraptor.hdf_parser (module)
riboraptor.helpers (module)
riboraptor.infer_protocol (module)
riboraptor.interval (module)
riboraptor.kmer (module)
riboraptor.normalization (module)
riboraptor.parallel (module)
riboraptor.plotting (module)
riboraptor.sequence (module)
riboraptor.sradb (module)
riboraptor.statistics (module)
riboraptor.tracks (module)
riboraptor.utils (module)
riboraptor.wig (module)
round_to_nearest() (in module riboraptor.helpers)
run_download_sra_script() (in module riboraptor.download)
S
scale_bigwig() (in module riboraptor.helpers)
search_experiment() (riboraptor.sradb.SRAdb method)
series_cdf() (in module riboraptor.statistics)
set_xrotation() (in module riboraptor.helpers)
setup_axis() (in module riboraptor.plotting)
setup_plot() (in module riboraptor.plotting)
sra_convert() (riboraptor.sradb.SRAdb method)
SRAdb (class in riboraptor.sradb)
summarize_counters() (in module riboraptor.helpers)
summary_starlogs_over_runs() (in module riboraptor.utils)
summary_stats_two_arrays_welch() (in module riboraptor.helpers)
symlink_force() (in module riboraptor.helpers)
T
text_progessbar() (in module riboraptor.parallel)
tsv_to_bigwig() (in module riboraptor.hdf_parser)
W
WigReader (class in riboraptor.wig)
write_config() (in module riboraptor.utils)
Y
yield_intervals() (in module riboraptor.helpers)
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