pyranges
master
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API Reference
pyranges
Index
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Index
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A
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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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J
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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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R
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S
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T
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U
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V
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W
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__array_ufunc__() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
__enter__() (pyranges.multithreaded.suppress_stdout_stderr method)
__exit__() (pyranges.multithreaded.suppress_stdout_stderr method)
__getattr__() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
__getitem__() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
__getstate__() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
__iter__() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
__len__() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
__repr__() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
__setattr__() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
__setstate__() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
__str__() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
_extend() (in module pyranges.multithreaded)
_extend_grp() (in module pyranges.multithreaded)
_fetch_gene_transcript_exon_id() (in module pyranges.readers)
_lengths() (in module pyranges.multithreaded)
_repr_html_() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
_tes() (in module pyranges.multithreaded)
_tss() (in module pyranges.multithreaded)
A
aorta() (in module pyranges.data)
aorta2() (in module pyranges.data)
apply() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
apply_chunks() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
apply_pair() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
as_df() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
assign() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
B
boundaries() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
C
calculate_frame() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
call_f() (in module pyranges.multithreaded)
call_f_single() (in module pyranges.multithreaded)
chipseq() (in module pyranges.data)
chipseq_background() (in module pyranges.data)
chromosomes (pyranges.PyRanges property)
(pyranges.pyranges_main.PyRanges property)
chromsizes() (in module pyranges.data)
cluster() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
columns (pyranges.PyRanges property)
(pyranges.pyranges_main.PyRanges property)
control_bam() (in module pyranges.data)
copy() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
count_overlaps() (in module pyranges)
(in module pyranges.multioverlap)
(pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
coverage() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
cpg() (in module pyranges.data)
D
df (pyranges.PyRanges property)
(pyranges.pyranges_main.PyRanges property)
dfs (pyranges.PyRanges attribute)
(pyranges.pyranges_main.PyRanges attribute)
drop() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
drop_duplicate_positions() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
dtypes (pyranges.PyRanges property)
(pyranges.pyranges_main.PyRanges property)
E
empty (pyranges.PyRanges property)
(pyranges.pyranges_main.PyRanges property)
ensembl_gtf() (in module pyranges.data)
exons() (in module pyranges.data)
extend() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
F
f1() (in module pyranges.data)
f2() (in module pyranges.data)
fdr() (in module pyranges.statistics)
features (pyranges.PyRanges attribute)
(pyranges.pyranges_main.PyRanges attribute)
fisher_exact() (in module pyranges.statistics)
five_end() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
forbes() (pyranges.statistics.StatisticsMethods method)
from_dict() (in module pyranges)
from_string() (in module pyranges)
G
gencode_gtf() (in module pyranges.data)
genome_bounds() (in module pyranges.genomicfeatures)
GenomicFeaturesMethods (class in pyranges.genomicfeatures)
get_chromosomes_from_dict() (in module pyranges.helpers)
get_fasta() (in module pyranges.get_fasta)
get_key_from_df() (in module pyranges.helpers)
get_multithreaded_funcs() (in module pyranges.multithreaded)
get_n_args() (in module pyranges.multithreaded)
get_sequence() (in module pyranges.get_fasta)
get_strands_from_dict() (in module pyranges.helpers)
get_transcript_sequence() (in module pyranges.get_fasta)
H
head() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
I
insert() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
intersect() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
introns() (pyranges.genomicfeatures.GenomicFeaturesMethods method)
items() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
itergrs() (in module pyranges)
J
jaccard() (pyranges.statistics.StatisticsMethods method)
join() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
K
k_nearest() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
keys() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
L
length (pyranges.PyRanges property)
(pyranges.pyranges_main.PyRanges property)
lengths() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
M
make_binary_sparse() (in module pyranges.multithreaded)
make_sparse() (in module pyranges.multithreaded)
make_unary_sparse() (in module pyranges.multithreaded)
max_disjoint() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
mcc() (in module pyranges.statistics)
merge() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
merge_dfs() (in module pyranges.multithreaded)
module
pyranges
pyranges.data
pyranges.genomicfeatures
pyranges.get_fasta
pyranges.helpers
pyranges.multioverlap
pyranges.multithreaded
pyranges.pyranges_main
pyranges.readers
pyranges.statistics
pyranges.stats
mp() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
mpc() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
msp() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
mspc() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
N
nearest() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
new_position() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
O
overlap() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
P
parse_kv_fields() (in module pyranges.readers)
pc() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
pr (pyranges.genomicfeatures.GenomicFeaturesMethods attribute)
(pyranges.statistics.StatisticsMethods attribute)
print() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
process_results() (in module pyranges.multithreaded)
pyrange_apply() (in module pyranges.multithreaded)
pyrange_apply_chunks() (in module pyranges.multithreaded)
pyrange_apply_single() (in module pyranges.multithreaded)
pyranges
module
PyRanges (class in pyranges)
(class in pyranges.pyranges_main)
pyranges.data
module
pyranges.genomicfeatures
module
pyranges.get_fasta
module
pyranges.helpers
module
pyranges.multioverlap
module
pyranges.multithreaded
module
pyranges.pyranges_main
module
pyranges.readers
module
pyranges.statistics
module
pyranges.stats
module
R
random() (in module pyranges)
ray (in module pyranges.multithreaded)
ray_initialized() (in module pyranges.multithreaded)
read_bam() (in module pyranges)
(in module pyranges.readers)
read_bed() (in module pyranges)
(in module pyranges.readers)
read_bigwig() (in module pyranges.readers)
read_gff3() (in module pyranges)
(in module pyranges.readers)
read_gtf() (in module pyranges)
(in module pyranges.readers)
read_gtf_full() (in module pyranges.readers)
read_gtf_restricted() (in module pyranges.readers)
relative_distance() (pyranges.statistics.StatisticsMethods method)
rename_core_attrs() (in module pyranges.readers)
rowbased_pearson() (in module pyranges.statistics)
rowbased_rankdata() (in module pyranges.statistics)
rowbased_spearman() (in module pyranges.statistics)
rp() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
rpc() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
S
sample() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
set_intersect() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
set_union() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
simes() (in module pyranges.statistics)
single_value_key() (in module pyranges.helpers)
skiprows() (in module pyranges.readers)
slack() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
sort() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
sp() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
spc() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
spliced_subsequence() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
split() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
StatisticsMethods (class in pyranges.statistics)
stats (pyranges.PyRanges attribute)
(pyranges.pyranges_main.PyRanges attribute)
stranded (pyranges.PyRanges property)
(pyranges.pyranges_main.PyRanges property)
strands (pyranges.PyRanges property)
(pyranges.pyranges_main.PyRanges property)
subsequence() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
subset() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
subtract() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
summary() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
suppress_stdout_stderr (class in pyranges.multithreaded)
T
tail() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
tes() (pyranges.genomicfeatures.GenomicFeaturesMethods method)
three_end() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
tile() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
tile_genome() (in module pyranges.genomicfeatures)
to_bed() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
to_bigwig() (in module pyranges)
(pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
to_csv() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
to_example() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
to_gff3() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
to_gtf() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
to_rle() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
to_rows() (in module pyranges.readers)
to_rows_gff3() (in module pyranges.readers)
to_rows_keep_duplicates() (in module pyranges.readers)
tss() (pyranges.genomicfeatures.GenomicFeaturesMethods method)
U
ucsc_bed() (in module pyranges.data)
unstrand() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
V
values() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
version_info() (in module pyranges)
W
window() (pyranges.PyRanges method)
(pyranges.pyranges_main.PyRanges method)
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