Python
latest
Guide
Quickstart
Genomic interval operations
Reading genomic dataframes
Performance
How do I
Definitions
Specifications
Bioframe for bedtools users
Tutorials
How to: assign TF Motifs to ChIP-seq peaks
How to: assign ChIP-seq peaks to genes
API
Construction
Validation
Interval operations
File I/O
Resources
Additional tools
Plotting
Low-level API
Python
Index
Edit on GitHub
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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I
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L
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M
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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
_
_get_default_colnames() (specs method)
_verify_column_dtypes() (specs method)
_verify_columns() (specs method)
A
alias_dict (GenomeAssembly attribute)
arange_multi() (in module bioframe.core.arrops)
assemblies_available() (in module bioframe.io.assembly)
assembly_info() (in module bioframe.io.assembly)
assign_view() (in module bioframe.ops)
B
binnify() (in module bioframe.extras)
bioframe.core.arrops
module
bioframe.core.checks
module
bioframe.core.construction
module
bioframe.core.specs
module
bioframe.core.stringops
module
bioframe.extras
module
bioframe.io.assembly
module
bioframe.io.fileops
module
bioframe.io.resources
module
bioframe.ops
module
bioframe.vis
module
C
chromnames (GenomeAssembly property)
chromsizes (GenomeAssembly property)
closest() (in module bioframe.ops)
closest_intervals() (in module bioframe.core.arrops)
cluster() (in module bioframe.ops)
complement() (in module bioframe.ops)
count_overlaps() (in module bioframe.ops)
coverage() (in module bioframe.ops)
cytobands (GenomeAssembly attribute)
D
digest() (in module bioframe.extras)
E
expand() (in module bioframe.ops)
F
fetch_centromeres() (in module bioframe.io.resources)
fetch_chromsizes() (in module bioframe.io.resources)
frac_gc() (in module bioframe.extras)
frac_gene_coverage() (in module bioframe.extras)
frac_mapped() (in module bioframe.extras)
from_any() (in module bioframe.core.construction)
from_dict() (in module bioframe.core.construction)
G
GenomeAssembly (class in bioframe.io.assembly)
I
interweave() (in module bioframe.core.arrops)
is_bedframe() (in module bioframe.core.checks)
is_cataloged() (in module bioframe.core.checks)
is_chrom_dtype() (in module bioframe.core.specs)
is_complete_ucsc_string() (in module bioframe.core.stringops)
is_contained() (in module bioframe.core.checks)
is_covering() (in module bioframe.core.checks)
is_overlapping() (in module bioframe.core.checks)
is_sorted() (in module bioframe.core.checks)
is_tiling() (in module bioframe.core.checks)
is_viewframe() (in module bioframe.core.checks)
L
load_fasta() (in module bioframe.io.fileops)
M
make_chromarms() (in module bioframe.extras)
make_viewframe() (in module bioframe.core.construction)
merge() (in module bioframe.ops)
merge_intervals() (in module bioframe.core.arrops)
module
bioframe.core.arrops
bioframe.core.checks
bioframe.core.construction
bioframe.core.specs
bioframe.core.stringops
bioframe.extras
bioframe.io.assembly
bioframe.io.fileops
bioframe.io.resources
bioframe.ops
bioframe.vis
O
organism (GenomeAssembly attribute)
overlap() (in module bioframe.ops)
overlap_intervals() (in module bioframe.core.arrops)
overlap_intervals_outer() (in module bioframe.core.arrops)
P
pair_by_distance() (in module bioframe.extras)
parse_region() (in module bioframe.core.stringops)
parse_region_string() (in module bioframe.core.stringops)
plot_intervals() (in module bioframe.vis)
provider (GenomeAssembly attribute)
provider_build (GenomeAssembly attribute)
R
read_bam() (in module bioframe.io.fileops)
read_bigbed() (in module bioframe.io.fileops)
read_bigwig() (in module bioframe.io.fileops)
read_chromsizes() (in module bioframe.io.fileops)
read_pairix() (in module bioframe.io.fileops)
read_tabix() (in module bioframe.io.fileops)
read_table() (in module bioframe.io.fileops)
release_year (GenomeAssembly attribute)
S
sanitize_bedframe() (in module bioframe.core.construction)
select() (in module bioframe.ops)
select_indices() (in module bioframe.ops)
select_labels() (in module bioframe.ops)
select_mask() (in module bioframe.ops)
seq_gc() (in module bioframe.extras)
seqinfo (GenomeAssembly attribute)
setdiff() (in module bioframe.ops)
sort_bedframe() (in module bioframe.ops)
subtract() (in module bioframe.ops)
sum_slices() (in module bioframe.core.arrops)
T
to_bed() (in module bioframe.io.bed)
to_bigbed() (in module bioframe.io.fileops)
to_bigwig() (in module bioframe.io.fileops)
to_ucsc_colorstring() (in module bioframe.vis)
to_ucsc_string() (in module bioframe.core.stringops)
trim() (in module bioframe.ops)
U
url (GenomeAssembly attribute)
V
viewframe (GenomeAssembly property)
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