Pyllelic
Contents:
Welcome to Pyllelic’s documentation!
Quickstart
Demo gif
Dependencies and Installation
Using Conda (preferred)
Docker container
PyPi installation
Quickstart
Example exploratory use in jupyter notebook
Function Reference
pyllelic package
Submodules
pyllelic.config module
pyllelic.process module
pyllelic.pyllelic module
pyllelic.quma module
pyllelic.visualization module
Authors
pyllelic package
Submodules
pyllelic.config module
pyllelic.process module
pyllelic.pyllelic module
pyllelic.quma module
pyllelic.visualization module
Pyllelic
»
Index
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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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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U
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V
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W
_
_create_heatmap() (in module pyllelic.visualization)
_create_histogram() (in module pyllelic.visualization)
_create_methylation_diffs_bar_graph() (in module pyllelic.visualization)
_make_binary() (in module pyllelic.visualization)
_make_methyl_df() (in module pyllelic.visualization)
_make_stacked_fig() (in module pyllelic.visualization)
_make_stacked_mpl_fig() (in module pyllelic.visualization)
_make_stacked_plotly_fig() (in module pyllelic.visualization)
A
AD_stats (class in pyllelic.pyllelic)
aliLen (pyllelic.quma.Result attribute)
aliMis (pyllelic.quma.Result attribute)
allelic_data (pyllelic.pyllelic.GenomicPositionData attribute)
analysis_directory (pyllelic.config.Config attribute)
B
BamOutput (class in pyllelic.pyllelic)
base_directory (pyllelic.config.Config attribute)
bismark() (in module pyllelic.process)
bowtie2_fastq_to_bam() (in module pyllelic.process)
build_bowtie2_index() (in module pyllelic.process)
C
cell_types (pyllelic.pyllelic.GenomicPositionData attribute)
chromosome (pyllelic.config.Config attribute)
com (pyllelic.quma.Fasta attribute)
Config (class in pyllelic.config)
config (pyllelic.pyllelic.GenomicPositionData attribute)
configure() (in module pyllelic.pyllelic)
conv (pyllelic.quma.Result attribute)
crits (pyllelic.pyllelic.AD_stats attribute)
D
data (pyllelic.quma.Quma attribute)
diffs (pyllelic.pyllelic.GenomicPositionData attribute)
dir (pyllelic.quma.Reference attribute)
E
exc (pyllelic.quma.Reference attribute)
F
Fasta (class in pyllelic.quma)
fasta (pyllelic.quma.Reference attribute)
fastq_to_list() (in module pyllelic.process)
file_names (pyllelic.pyllelic.GenomicPositionData attribute)
files_set (pyllelic.pyllelic.GenomicPositionData attribute)
fname_pattern (pyllelic.config.Config attribute)
from_pickle() (pyllelic.pyllelic.GenomicPositionData static method)
G
gAli (pyllelic.quma.Result attribute)
gap (pyllelic.quma.Result attribute)
gdir (pyllelic.quma.Reference attribute)
generate_ad_stats() (pyllelic.pyllelic.GenomicPositionData method)
genome_values (pyllelic.pyllelic.BamOutput attribute)
GenomicPositionData (class in pyllelic.pyllelic)
H
heatmap() (pyllelic.pyllelic.GenomicPositionData method)
histogram() (pyllelic.pyllelic.GenomicPositionData method)
I
index_bam() (in module pyllelic.process)
individual_data (pyllelic.pyllelic.GenomicPositionData attribute)
M
make_list_of_bam_files() (in module pyllelic.pyllelic)
make_records_to_dictionary() (in module pyllelic.process)
match (pyllelic.quma.Result attribute)
means (pyllelic.pyllelic.GenomicPositionData attribute)
menum (pyllelic.quma.Result attribute)
modes (pyllelic.pyllelic.GenomicPositionData attribute)
module
pyllelic.config
pyllelic.process
pyllelic.pyllelic
pyllelic.quma
pyllelic.visualization
N
name (pyllelic.pyllelic.BamOutput attribute)
O
offset (pyllelic.config.Config attribute)
P
pconv (pyllelic.quma.Result attribute)
perc (pyllelic.quma.Result attribute)
pos (pyllelic.quma.Fasta attribute)
positions (pyllelic.pyllelic.BamOutput attribute)
(pyllelic.pyllelic.GenomicPositionData attribute)
prepare_genome() (in module pyllelic.process)
promoter_end (pyllelic.config.Config attribute)
promoter_file (pyllelic.config.Config attribute)
promoter_start (pyllelic.config.Config attribute)
pyllelic() (in module pyllelic.pyllelic)
pyllelic.config
module
pyllelic.process
module
pyllelic.pyllelic
module
pyllelic.quma
module
pyllelic.visualization
module
Q
qAli (pyllelic.quma.Result attribute)
Quma (class in pyllelic.quma)
quma_output (pyllelic.pyllelic.QumaResult attribute)
quma_results (pyllelic.pyllelic.GenomicPositionData attribute)
QumaResult (class in pyllelic.pyllelic)
R
reads_graph() (pyllelic.pyllelic.GenomicPositionData method)
Reference (class in pyllelic.quma)
res (pyllelic.quma.Reference attribute)
Result (class in pyllelic.quma)
results_directory (pyllelic.config.Config attribute)
retrieve_seq() (in module pyllelic.process)
S
save() (pyllelic.pyllelic.GenomicPositionData method)
save_pickle() (pyllelic.pyllelic.GenomicPositionData method)
seq (pyllelic.quma.Fasta attribute)
ShellCommandError
sig (pyllelic.pyllelic.AD_stats attribute)
sig_methylation_differences() (pyllelic.pyllelic.GenomicPositionData method)
sort_bam() (in module pyllelic.process)
stat (pyllelic.pyllelic.AD_stats attribute)
summarize_allelic_data() (pyllelic.pyllelic.GenomicPositionData method)
U
unconv (pyllelic.quma.Result attribute)
V
val (pyllelic.quma.Result attribute)
values (pyllelic.pyllelic.BamOutput attribute)
(pyllelic.pyllelic.QumaResult attribute)
(pyllelic.quma.Quma attribute)
viz_backend (pyllelic.config.Config attribute)
W
write_means_modes_diffs() (pyllelic.pyllelic.GenomicPositionData method)