bionumpy
1.0.11
Home
BioNumPy at a glance
Getting started with BioNumPy in 10 minutes
Using BioNumPy in your existing project
Tutorials
Filtering FASTQ reads
Working with BAM-files
Getting read pileup inside peaks (intervals)
FastQC-like quality-checking of FASTQ files
Computing GC content inside genes
Position Weight Matrix
Simulating sequence datasets
Computing the similarity between two BED-files
Extracting kmers around snps
Interoperability
Numpy Interoperability
Using BioNumPy with Biopython
Pandas Interoperability
BioNumPy Concepts
Reading files
Encodings
Supported file formats
Reading a new file format
Sequences
Intervals
Working with Multiple Files/Data Sources
Broadcastable Functions
API documentation
BnpDataclass
Genome arithmetics
Genomic Data
IO
Sequences
Streams
Other
Developer guide
BioNumPy manuscript
bionumpy
Index
Index
B
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C
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E
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F
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G
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I
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J
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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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W
B
BedBuffer (class in bionumpy.io)
bnp_open() (in module bionumpy.io)
bnpdataclass() (in module bionumpy.bnpdataclass)
C
calculate_score() (bionumpy.sequence.PWM method)
calculate_scores() (bionumpy.sequence.PWM method)
clip() (bionumpy.genomic_data.GenomicIntervals method)
count_encoded() (in module bionumpy.sequence)
count_entries() (in module bionumpy.io)
E
extended_to_size() (bionumpy.genomic_data.GenomicIntervals method)
extract_intervals() (bionumpy.genomic_data.GenomicSequence method)
F
FastQBuffer (class in bionumpy.io)
forbes() (in module bionumpy.arithmetics)
from_bedgraph() (bionumpy.genomic_data.GenomicArray class method)
from_counts() (bionumpy.sequence.PWM class method)
from_data() (bionumpy.genomic_data.GenomicLocation class method)
from_dict() (bionumpy.genomic_data.Genome class method)
(bionumpy.genomic_data.GenomicSequence class method)
(bionumpy.sequence.PWM class method)
from_fields() (bionumpy.genomic_data.GenomicIntervals class method)
(bionumpy.genomic_data.GenomicLocation class method)
from_file() (bionumpy.genomic_data.Genome class method)
from_global_data() (bionumpy.genomic_data.GenomicArray class method)
from_gtf_entries() (bionumpy.genomic_data.GenomicAnnotation class method)
from_interval_stream() (bionumpy.genomic_data.GenomicIntervals class method)
from_intervals() (bionumpy.genomic_data.GenomicIntervals class method)
from_track() (bionumpy.genomic_data.GenomicIntervals class method)
G
Genome (class in bionumpy.genomic_data)
GenomicAnnotation (class in bionumpy.genomic_data)
GenomicArray (class in bionumpy.genomic_data)
GenomicIntervals (class in bionumpy.genomic_data)
GenomicLocation (class in bionumpy.genomic_data)
GenomicSequence (class in bionumpy.genomic_data)
get_boolean_mask() (in module bionumpy.arithmetics)
get_contig_lengths() (bionumpy.io.IndexedFasta method)
get_genome_context() (bionumpy.genomic_data.Genome method)
get_interval_sequences() (bionumpy.io.IndexedFasta method)
get_intervals() (bionumpy.genomic_data.Genome method)
get_kmers() (in module bionumpy.sequence)
get_locations() (bionumpy.genomic_data.Genome method)
get_mask() (bionumpy.genomic_data.GenomicIntervals method)
get_minimizers() (in module bionumpy.sequence)
get_motif_scores() (in module bionumpy.sequence)
get_pileup() (bionumpy.genomic_data.GenomicIntervals method)
(in module bionumpy.arithmetics)
get_track() (bionumpy.genomic_data.Genome method)
I
IndexedFasta (class in bionumpy.io)
J
jaccard() (in module bionumpy.arithmetics)
M
make_dataclass() (in module bionumpy.bnpdataclass)
match_string() (in module bionumpy.sequence)
merge_intervals() (in module bionumpy.arithmetics)
merged() (bionumpy.genomic_data.GenomicIntervals method)
O
open_indexed() (in module bionumpy.io)
P
PWM (class in bionumpy.sequence)
R
read_annotation() (bionumpy.genomic_data.Genome method)
read_intervals() (bionumpy.genomic_data.Genome method)
read_locations() (bionumpy.genomic_data.Genome method)
read_sequence() (bionumpy.genomic_data.Genome method)
read_track() (bionumpy.genomic_data.Genome method)
replace() (in module bionumpy.bnpdataclass)
S
size (bionumpy.genomic_data.Genome property)
sort_intervals() (in module bionumpy.arithmetics)
streamable() (in module bionumpy.streams)
T
TwoLineFastaBuffer (class in bionumpy.io)
V
VCFBuffer (class in bionumpy.io)
W
with_ignored_added() (bionumpy.genomic_data.Genome method)