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Contents:
README
Glossary
CLI
API
Tutorials
Changelog
fuc
Index
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Index
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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K
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L
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M
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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
A
add_af() (fuc.api.pyvcf.VcfFrame method)
add_dp() (fuc.api.pyvcf.VcfFrame method)
add_flag() (fuc.api.pyvcf.VcfFrame method)
aggregate() (fuc.api.pykallisto.KallistoFrame method)
AnnFrame (class in fuc.api.common)
annot_names() (in module fuc.api.pyvep)
AxiomFrame (class in fuc.api.pychip)
B
basic_filter() (in module fuc.api.pykallisto)
BedFrame (class in fuc.api.pybed)
C
calculate_concordance() (fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
call() (in module fuc.api.pyvcf)
collapse() (fuc.api.pyvcf.VcfFrame method)
color_print() (in module fuc.api.common)
combine() (fuc.api.pyvcf.VcfFrame method)
compare() (fuc.api.pyvcf.VcfFrame method)
compute_clonality() (fuc.api.pymaf.MafFrame method)
compute_fold_change() (fuc.api.pykallisto.KallistoFrame method)
compute_info() (fuc.api.pyvcf.VcfFrame method)
concat() (in module fuc.api.pycov)
conda_env() (in module fuc.api.common)
contigs (fuc.api.pybed.BedFrame property)
(fuc.api.pycov.CovFrame property)
(fuc.api.pyvcf.VcfFrame property)
convert_file2list() (in module fuc.api.common)
convert_num2cat() (in module fuc.api.common)
copy() (fuc.api.pycov.CovFrame method)
(fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
copy_df() (fuc.api.pycov.CovFrame method)
(fuc.api.pyvcf.VcfFrame method)
copy_meta() (fuc.api.pybed.BedFrame method)
(fuc.api.pyvcf.VcfFrame method)
count_allelic_depth() (in module fuc.api.pybam)
CovFrame (class in fuc.api.pycov)
D
df (fuc.api.common.AnnFrame property)
(fuc.api.pychip.AxiomFrame property)
(fuc.api.pychip.InfiniumFrame property)
(fuc.api.pycov.CovFrame property)
(fuc.api.pygff.GffFrame property)
(fuc.api.pyvcf.VcfFrame property)
diploidize() (fuc.api.pyvcf.VcfFrame method)
drop_duplicates() (fuc.api.pyvcf.VcfFrame method)
duplicated() (fuc.api.pyvcf.VcfFrame method)
E
empty (fuc.api.pyvcf.VcfFrame property)
empty_samples() (fuc.api.pyvcf.VcfFrame method)
expand() (fuc.api.pyvcf.VcfFrame method)
extract_format() (fuc.api.pyvcf.VcfFrame method)
extract_info() (fuc.api.pyvcf.VcfFrame method)
extract_sequence() (in module fuc.api.common)
F
fasta (fuc.api.pygff.GffFrame property)
fetch() (fuc.api.pyvcf.VcfFrame method)
filter_ann() (in module fuc.api.pysnpeff)
filter_annot() (fuc.api.pymaf.MafFrame method)
filter_bed() (fuc.api.pyvcf.VcfFrame method)
filter_empty() (fuc.api.pyvcf.VcfFrame method)
filter_flagall() (fuc.api.pyvcf.VcfFrame method)
filter_flagany() (fuc.api.pyvcf.VcfFrame method)
filter_gsa() (fuc.api.pyvcf.VcfFrame method)
filter_indel() (fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
filter_multialt() (fuc.api.pyvcf.VcfFrame method)
filter_pass() (fuc.api.pyvcf.VcfFrame method)
filter_phased() (fuc.api.pyvcf.VcfFrame method)
filter_polyp() (fuc.api.pyvcf.VcfFrame method)
filter_qual() (fuc.api.pyvcf.VcfFrame method)
filter_query() (in module fuc.api.pyvep)
filter_sampall() (fuc.api.pyvcf.VcfFrame method)
filter_sampany() (fuc.api.pyvcf.VcfFrame method)
filter_sampnum() (fuc.api.pyvcf.VcfFrame method)
filter_vcf() (fuc.api.pyvcf.VcfFrame method)
FqFrame (class in fuc.api.pyfq)
from_bam() (fuc.api.pycov.CovFrame class method)
from_dict() (fuc.api.common.AnnFrame class method)
(fuc.api.pybed.BedFrame class method)
(fuc.api.pycov.CovFrame class method)
(fuc.api.pyvcf.VcfFrame class method)
from_file() (fuc.api.common.AnnFrame class method)
(fuc.api.pybed.BedFrame class method)
(fuc.api.pychip.AxiomFrame class method)
(fuc.api.pychip.InfiniumFrame class method)
(fuc.api.pycov.CovFrame class method)
(fuc.api.pyfq.FqFrame class method)
(fuc.api.pygff.GffFrame class method)
(fuc.api.pymaf.MafFrame class method)
(fuc.api.pyvcf.VcfFrame class method)
from_frame() (fuc.api.pybed.BedFrame class method)
from_regions() (fuc.api.pybed.BedFrame class method)
from_string() (fuc.api.pyvcf.VcfFrame class method)
from_vcf() (fuc.api.pymaf.MafFrame class method)
fuc.api.common
module
fuc.api.pybam
module
fuc.api.pybed
module
fuc.api.pychip
module
fuc.api.pycov
module
fuc.api.pyfq
module
fuc.api.pygff
module
fuc.api.pykallisto
module
fuc.api.pymaf
module
fuc.api.pysnpeff
module
fuc.api.pyvcf
module
fuc.api.pyvep
module
G
genes (fuc.api.pymaf.MafFrame property)
get_af() (fuc.api.pyvcf.VcfFrame method)
get_gene_concordance() (fuc.api.pymaf.MafFrame method)
get_most_similar() (in module fuc.api.common)
get_similarity() (in module fuc.api.common)
GffFrame (class in fuc.api.pygff)
gr (fuc.api.pybed.BedFrame property)
gt_diploidize() (in module fuc.api.pyvcf)
gt_hasvar() (in module fuc.api.pyvcf)
gt_het() (in module fuc.api.pyvcf)
gt_miss() (in module fuc.api.pyvcf)
gt_ploidy() (in module fuc.api.pyvcf)
gt_polyp() (in module fuc.api.pyvcf)
gt_pseudophase() (in module fuc.api.pyvcf)
gt_unphase() (in module fuc.api.pyvcf)
H
has_chr_prefix (fuc.api.pybed.BedFrame property)
(fuc.api.pycov.CovFrame property)
(fuc.api.pyvcf.VcfFrame property)
has_chr_prefix() (in module fuc.api.pybam)
(in module fuc.api.pyvcf)
I
index() (in module fuc.api.pybam)
InfiniumFrame (class in fuc.api.pychip)
intersect() (fuc.api.pybed.BedFrame method)
is_similar() (in module fuc.api.common)
K
KallistoFrame (class in fuc.api.pykallisto)
L
legend_handles() (in module fuc.api.common)
load_dataset() (in module fuc.api.common)
M
MafFrame (class in fuc.api.pymaf)
markmiss() (fuc.api.pyvcf.VcfFrame method)
mask_bed() (fuc.api.pycov.CovFrame method)
matrix_genes() (fuc.api.pymaf.MafFrame method)
matrix_prevalence() (fuc.api.pymaf.MafFrame method)
matrix_tmb() (fuc.api.pymaf.MafFrame method)
matrix_uniformity() (fuc.api.pycov.CovFrame method)
matrix_waterfall() (fuc.api.pymaf.MafFrame method)
matrix_waterfall_matched() (fuc.api.pymaf.MafFrame method)
merge() (fuc.api.pybed.BedFrame method)
(fuc.api.pycov.CovFrame method)
(fuc.api.pyvcf.VcfFrame method)
(in module fuc.api.pycov)
(in module fuc.api.pyvcf)
meta (fuc.api.pybed.BedFrame property)
(fuc.api.pychip.AxiomFrame property)
(fuc.api.pygff.GffFrame property)
(fuc.api.pyvcf.VcfFrame property)
meta_keys() (fuc.api.pyvcf.VcfFrame method)
miss2ref() (fuc.api.pyvcf.VcfFrame method)
module
fuc.api.common
fuc.api.pybam
fuc.api.pybed
fuc.api.pychip
fuc.api.pycov
fuc.api.pyfq
fuc.api.pygff
fuc.api.pykallisto
fuc.api.pymaf
fuc.api.pysnpeff
fuc.api.pyvcf
fuc.api.pyvep
P
parse_list_or_file() (in module fuc.api.common)
parse_region() (in module fuc.api.common)
parse_variant() (in module fuc.api.common)
parseann() (in module fuc.api.pysnpeff)
(in module fuc.api.pyvep)
phased (fuc.api.pyvcf.VcfFrame property)
pick_result() (in module fuc.api.pyvep)
plot_af_correlation() (in module fuc.api.pyvcf)
plot_annot() (fuc.api.common.AnnFrame method)
plot_annot_matched() (fuc.api.common.AnnFrame method)
plot_clonality() (fuc.api.pymaf.MafFrame method)
plot_comparison() (fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
plot_cytobands() (in module fuc.api.common)
plot_differential_abundance() (fuc.api.pykallisto.KallistoFrame method)
plot_distribution() (fuc.api.pycov.CovFrame method)
plot_evolution() (fuc.api.pymaf.MafFrame method)
plot_exons() (in module fuc.api.common)
plot_genepair() (fuc.api.pymaf.MafFrame method)
plot_genes() (fuc.api.pymaf.MafFrame method)
plot_hist_format() (fuc.api.pyvcf.VcfFrame method)
plot_hist_info() (fuc.api.pyvcf.VcfFrame method)
plot_interactions() (fuc.api.pymaf.MafFrame method)
plot_lollipop() (fuc.api.pymaf.MafFrame method)
plot_matrixg() (fuc.api.pymaf.MafFrame method)
plot_matrixs() (fuc.api.pymaf.MafFrame method)
plot_mutated() (fuc.api.pymaf.MafFrame method)
plot_mutated_matched() (fuc.api.pymaf.MafFrame method)
plot_oncoplot() (fuc.api.pymaf.MafFrame method)
plot_oncoplot_matched() (fuc.api.pymaf.MafFrame method)
plot_rainfall() (fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
plot_region() (fuc.api.pycov.CovFrame method)
(fuc.api.pyvcf.VcfFrame method)
plot_regplot_gene() (fuc.api.pymaf.MafFrame method)
plot_regplot_tmb() (fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
plot_snvclsc() (fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
plot_snvclsp() (fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
plot_snvclss() (fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
plot_summary() (fuc.api.pymaf.MafFrame method)
plot_titv() (fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
plot_tmb() (fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
plot_tmb_matched() (fuc.api.pymaf.MafFrame method)
plot_uniformity() (fuc.api.pycov.CovFrame method)
plot_vaf() (fuc.api.pymaf.MafFrame method)
plot_varcls() (fuc.api.pymaf.MafFrame method)
plot_varsum() (fuc.api.pymaf.MafFrame method)
plot_vartype() (fuc.api.pymaf.MafFrame method)
plot_waterfall() (fuc.api.pymaf.MafFrame method)
plot_waterfall_matched() (fuc.api.pymaf.MafFrame method)
protein_length() (fuc.api.pygff.GffFrame method)
pseudophase() (fuc.api.pyvcf.VcfFrame method)
R
readlen() (fuc.api.pyfq.FqFrame method)
rename() (fuc.api.pycov.CovFrame method)
(fuc.api.pyvcf.VcfFrame method)
(in module fuc.api.common)
rescue_filtered_variants() (in module fuc.api.pyvcf)
reverse_complement() (in module fuc.api.common)
row_computeinfo() (in module fuc.api.pyvcf)
row_firstann() (in module fuc.api.pysnpeff)
(in module fuc.api.pyvep)
row_hasindel() (in module fuc.api.pyvcf)
row_missval() (in module fuc.api.pyvcf)
row_mostsevere() (in module fuc.api.pyvep)
row_parseinfo() (in module fuc.api.pyvcf)
row_phased() (in module fuc.api.pyvcf)
row_updateinfo() (in module fuc.api.pyvcf)
S
samples (fuc.api.common.AnnFrame property)
(fuc.api.pycov.CovFrame property)
(fuc.api.pymaf.MafFrame property)
(fuc.api.pyvcf.VcfFrame property)
shape (fuc.api.common.AnnFrame property)
(fuc.api.pybed.BedFrame property)
(fuc.api.pycov.CovFrame property)
(fuc.api.pyfq.FqFrame property)
(fuc.api.pymaf.MafFrame property)
(fuc.api.pyvcf.VcfFrame property)
simulate() (in module fuc.api.pycov)
sites_only (fuc.api.pyvcf.VcfFrame property)
slice() (fuc.api.pycov.CovFrame method)
(fuc.api.pyvcf.VcfFrame method)
(in module fuc.api.pybam)
(in module fuc.api.pyvcf)
sort() (fuc.api.pybed.BedFrame method)
(fuc.api.pyvcf.VcfFrame method)
sort_regions() (in module fuc.api.common)
sort_variants() (in module fuc.api.common)
sorted_samples() (fuc.api.common.AnnFrame method)
split() (in module fuc.api.pyvcf)
strip() (fuc.api.pyvcf.VcfFrame method)
subset() (fuc.api.common.AnnFrame method)
(fuc.api.pycov.CovFrame method)
(fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
subtract() (fuc.api.pyvcf.VcfFrame method)
sumstat() (in module fuc.api.common)
T
tag_sm() (in module fuc.api.pybam)
tag_sn() (in module fuc.api.pybam)
to_bed() (fuc.api.pyvcf.VcfFrame method)
to_file() (fuc.api.pybed.BedFrame method)
(fuc.api.pycov.CovFrame method)
(fuc.api.pyfq.FqFrame method)
(fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
to_frame() (in module fuc.api.pyvep)
to_regions() (fuc.api.pybed.BedFrame method)
to_string() (fuc.api.pybed.BedFrame method)
(fuc.api.pycov.CovFrame method)
(fuc.api.pymaf.MafFrame method)
(fuc.api.pyvcf.VcfFrame method)
to_variants() (fuc.api.pyvcf.VcfFrame method)
to_vcf() (fuc.api.pymaf.MafFrame method)
to_vep() (fuc.api.pychip.AxiomFrame method)
(fuc.api.pychip.InfiniumFrame method)
U
unphase() (fuc.api.pyvcf.VcfFrame method)
update_chr_prefix() (fuc.api.pybed.BedFrame method)
(fuc.api.pycov.CovFrame method)
(fuc.api.pyvcf.VcfFrame method)
(in module fuc.api.common)
V
variants() (fuc.api.pymaf.MafFrame method)
VcfFrame (class in fuc.api.pyvcf)
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