RNFtools
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2. Tutorials
3. Reference
4. Additional information
RNFtools
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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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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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V
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W
A
add_graph() (rnftools.lavender.Report.Report method)
add_read() (rnftools.rnfformat.FqCreator.FqCreator method)
apply() (rnftools.rnfformat.RnfProfile.RnfProfile method)
ArtIllumina (class in rnftools.mishmash.ArtIllumina)
B
Bam (class in rnftools.lavender.Bam)
bam2es() (rnftools.lavender.Bam.Bam static method)
bam_fn() (rnftools.lavender.Bam.Bam method)
C
check() (rnftools.rnfformat.RnfProfile.RnfProfile method)
chr_id_width (rnftools.rnfformat.RnfProfile.RnfProfile attribute)
clean() (rnftools.lavender.Report.Report method)
(rnftools.mishmash.Source.Source method)
combine() (rnftools.rnfformat.RnfProfile.RnfProfile method)
coor_width (rnftools.rnfformat.RnfProfile.RnfProfile attribute)
create_es() (rnftools.lavender.Bam.Bam method)
create_et() (rnftools.lavender.Bam.Bam method)
create_fa() (rnftools.mishmash.Source.Source method)
create_fq() (rnftools.mishmash.ArtIllumina.ArtIllumina method)
(rnftools.mishmash.CuReSim.CuReSim method)
(rnftools.mishmash.DwgSim.DwgSim method)
(rnftools.mishmash.MasonIllumina.MasonIllumina method)
(rnftools.mishmash.Source.Source method)
(rnftools.mishmash.WgSim.WgSim method)
create_gp() (rnftools.lavender.Bam.Bam method)
(rnftools.lavender.Panel.Panel method)
create_graphics() (rnftools.lavender.Bam.Bam method)
(rnftools.lavender.Panel.Panel method)
create_html() (rnftools.lavender.Bam.Bam method)
(rnftools.lavender.Report.Report method)
create_roc() (rnftools.lavender.Bam.Bam method)
create_tar() (rnftools.lavender.Panel.Panel method)
CuReSim (class in rnftools.mishmash.CuReSim)
D
destringize() (rnftools.rnfformat.ReadTuple.ReadTuple method)
(rnftools.rnfformat.Segment.Segment method)
DwgSim (class in rnftools.mishmash.DwgSim)
E
empty() (rnftools.rnfformat.FqCreator.FqCreator method)
es2et() (rnftools.lavender.Bam.Bam static method)
es_fn() (rnftools.lavender.Bam.Bam method)
et2roc() (rnftools.lavender.Bam.Bam static method)
et_fn() (rnftools.lavender.Bam.Bam method)
F
fa0_fn() (rnftools.mishmash.Source.Source method)
fa_fn() (rnftools.mishmash.Source.Source method)
flush_read_tuple() (rnftools.rnfformat.FqCreator.FqCreator method)
fq_fn() (rnftools.mishmash.Source.Source method)
FqCreator (class in rnftools.rnfformat.FqCreator)
FqMerger (class in rnftools.rnfformat.FqMerger)
G
genome_id_width (rnftools.rnfformat.RnfProfile.RnfProfile attribute)
get_bams() (rnftools.lavender.Panel.Panel method)
get_dir() (rnftools.mishmash.Source.Source method)
get_genome_id() (rnftools.mishmash.Source.Source method)
get_html_column() (rnftools.lavender.Panel.Panel method)
get_input() (rnftools.mishmash.ArtIllumina.ArtIllumina method)
(rnftools.mishmash.CuReSim.CuReSim method)
(rnftools.mishmash.DwgSim.DwgSim method)
(rnftools.mishmash.MasonIllumina.MasonIllumina method)
(rnftools.mishmash.Source.Source method)
(rnftools.mishmash.WgSim.WgSim method)
get_name() (rnftools.lavender.Bam.Bam method)
get_number_of_required_cores() (rnftools.mishmash.Source.Source method)
get_output() (rnftools.mishmash.ArtIllumina.ArtIllumina method)
(rnftools.mishmash.CuReSim.CuReSim method)
(rnftools.mishmash.DwgSim.DwgSim method)
(rnftools.mishmash.MasonIllumina.MasonIllumina method)
(rnftools.mishmash.Source.Source method)
(rnftools.mishmash.WgSim.WgSim method)
get_panel_dir() (rnftools.lavender.Panel.Panel method)
get_panels() (rnftools.lavender.Report.Report method)
get_reads_in_tuple() (rnftools.mishmash.Source.Source method)
get_report() (rnftools.lavender.Panel.Panel method)
get_report_dir() (rnftools.lavender.Report.Report method)
get_required_files() (rnftools.lavender.Bam.Bam method)
(rnftools.lavender.Panel.Panel method)
get_return_code() (rnftools.rnfformat.Validator.Validator method)
get_rnf_name() (rnftools.rnfformat.RnfProfile.RnfProfile method)
gp_fn() (rnftools.lavender.Bam.Bam method)
(rnftools.lavender.Panel.Panel method)
H
html_fn() (rnftools.lavender.Bam.Bam method)
(rnftools.lavender.Report.Report method)
I
is_empty() (rnftools.rnfformat.FqCreator.FqCreator method)
L
load() (rnftools.rnfformat.RnfProfile.RnfProfile method)
M
MasonIllumina (class in rnftools.mishmash.MasonIllumina)
P
Panel (class in rnftools.lavender.Panel)
pdf_fn() (rnftools.lavender.Bam.Bam method)
prefix_width (rnftools.rnfformat.RnfProfile.RnfProfile attribute)
R
read_tuple_id_width (rnftools.rnfformat.RnfProfile.RnfProfile attribute)
ReadTuple (class in rnftools.rnfformat.ReadTuple)
recode_curesim_reads() (rnftools.mishmash.CuReSim.CuReSim static method)
recode_dwgsim_reads() (rnftools.mishmash.DwgSim.DwgSim static method)
recode_sam_reads() (rnftools.mishmash.Source.Source static method)
recode_wgsim_reads() (rnftools.mishmash.WgSim.WgSim static method)
Report (class in rnftools.lavender.Report)
report_error() (rnftools.rnfformat.Validator.Validator method)
RnfProfile (class in rnftools.rnfformat.RnfProfile)
roc_fn() (rnftools.lavender.Bam.Bam method)
run() (rnftools.rnfformat.FqMerger.FqMerger method)
S
Segment (class in rnftools.rnfformat.Segment)
Source (class in rnftools.mishmash.Source)
stringize() (rnftools.rnfformat.ReadTuple.ReadTuple method)
(rnftools.rnfformat.Segment.Segment method)
svg_fn() (rnftools.lavender.Bam.Bam method)
svg_fns() (rnftools.lavender.Panel.Panel method)
T
tar_fn() (rnftools.lavender.Panel.Panel method)
V
validate() (rnftools.rnfformat.Validator.Validator method)
Validator (class in rnftools.rnfformat.Validator)
W
WgSim (class in rnftools.mishmash.WgSim)
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