Index
A
|
C
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
O
|
P
|
R
|
S
|
T
|
U
|
V
A
align() (in module mirtop.mirna.realign)
align_from_variants() (in module mirtop.mirna.realign)
annotate() (in module mirtop.mirna.annotate)
C
chdir() (in module mirtop.libs.utils)
check_multiple() (in module mirtop.gff.validator)
cigar2snp() (in module mirtop.mirna.realign)
cigar2variants() (in module mirtop.importer.isomirsea)
cigar_2_key() (in module mirtop.exporter.vcf)
cigar_correction() (in module mirtop.mirna.realign)
clean_hits() (in module mirtop.bam.filter)
compare() (in module mirtop.gff.compare)
convert() (in module mirtop.exporter.fasta)
(in module mirtop.exporter.isomirs)
(in module mirtop.exporter.vcf)
(in module mirtop.gff.update)
create() (in module mirtop.gff.body)
(in module mirtop.gff.header)
create_vcf() (in module mirtop.exporter.vcf)
(in module mirtop.mirna.snps)
E
expand_cigar() (in module mirtop.mirna.realign)
F
file_exists() (in module mirtop.libs.utils)
find_bash() (in module mirtop.libs.do)
find_cmd() (in module mirtop.libs.do)
format() (mirtop.mirna.realign.isomir method)
,
[1]
format_id() (mirtop.mirna.realign.isomir method)
,
[1]
formatGFF() (mirtop.mirna.realign.isomir method)
,
[1]
G
get_mature_sequence() (in module mirtop.mirna.realign)
get_primary_transcript() (in module mirtop.mirna.mapper)
get_score() (mirtop.mirna.realign.isomir method)
,
[1]
guess_database() (in module mirtop.mirna.mapper)
H
header() (in module mirtop.importer.isomirsea)
(in module mirtop.importer.prost)
(in module mirtop.importer.seqbuster)
hits (class in mirtop.mirna.realign)
,
[1]
I
is_fastq() (in module mirtop.libs.fastq)
is_iso() (mirtop.mirna.realign.isomir method)
,
[1]
is_sequence() (in module mirtop.mirna.realign)
isomir (class in mirtop.mirna.realign)
,
[1]
L
lift_to_genome() (in module mirtop.gff.body)
liftover() (in module mirtop.mirna.snps)
liftover_to_genome() (in module mirtop.mirna.snps)
M
make_cigar() (in module mirtop.mirna.realign)
make_id() (in module mirtop.mirna.realign)
merge() (in module mirtop.gff.merge)
mirtop (module)
mirtop.bam.filter (module)
mirtop.exporter.fasta (module)
mirtop.exporter.isomirs (module)
mirtop.exporter.vcf (module)
mirtop.gff.body (module)
mirtop.gff.compare (module)
mirtop.gff.header (module)
mirtop.gff.merge (module)
mirtop.gff.stats (module)
mirtop.gff.update (module)
mirtop.gff.validator (module)
mirtop.importer.isomirsea (module)
mirtop.importer.manatee (module)
mirtop.importer.optimir (module)
mirtop.importer.prost (module)
mirtop.importer.seqbuster (module)
mirtop.importer.srnabench (module)
mirtop.libs.do (module)
mirtop.libs.fastq (module)
mirtop.libs.parse (module)
mirtop.libs.utils (module)
mirtop.mirna.annotate (module)
mirtop.mirna.fasta (module)
mirtop.mirna.keys (module)
mirtop.mirna.mapper (module)
mirtop.mirna.realign (module)
mirtop.mirna.snps (module)
O
open_fastq() (in module mirtop.libs.fastq)
P
parse_cl() (in module mirtop.libs.parse)
paste_columns() (in module mirtop.gff.body)
print_vcf() (in module mirtop.mirna.snps)
R
read() (in module mirtop.gff.body)
read_file() (in module mirtop.importer.isomirsea)
(in module mirtop.importer.manatee)
(in module mirtop.importer.optimir)
(in module mirtop.importer.prost)
(in module mirtop.importer.seqbuster)
(in module mirtop.importer.srnabench)
read_gff_line() (in module mirtop.gff.body)
read_gtf_chr2mirna() (in module mirtop.mirna.mapper)
read_gtf_to_mirna() (in module mirtop.mirna.mapper)
read_gtf_to_precursor() (in module mirtop.mirna.mapper)
read_gtf_to_precursor_mirbase() (in module mirtop.mirna.mapper)
read_gtf_to_precursor_mirgenedb() (in module mirtop.mirna.mapper)
read_id() (in module mirtop.mirna.realign)
read_precursor() (in module mirtop.mirna.fasta)
read_reference() (in module mirtop.gff.compare)
read_samples() (in module mirtop.gff.header)
read_variant() (in module mirtop.gff.body)
read_version() (in module mirtop.gff.header)
reverse_complement() (in module mirtop.mirna.realign)
run() (in module mirtop.libs.do)
S
safe_dirs() (in module mirtop.libs.utils)
safe_remove() (in module mirtop.libs.utils)
set_pos() (mirtop.mirna.realign.isomir method)
,
[1]
splitext_plus() (in module mirtop.libs.fastq)
stats() (in module mirtop.gff.stats)
T
tune() (in module mirtop.bam.filter)
U
update_file() (in module mirtop.gff.update)
V
variant_to_3p() (in module mirtop.mirna.realign)
variant_to_5p() (in module mirtop.mirna.realign)
variant_to_add() (in module mirtop.mirna.realign)
variant_with_nt() (in module mirtop.gff.body)
mirtop
API to work with GFF3 sRNA-data files
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