Bipype
latest
Code
CLI
DESCRIPTION
Appendixes
Bipype
Docs
»
Edit on GitHub
Index
Symbols
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
X
Symbols
--cutadapt <adapter_file> <search_options>
command line option
--db_16S <database>
command line option
--db_ITS <database>
command line option
--db_NCBI_taxonomy
command line option
--db_reconstruct
command line option
--db_refseq_fungi <databases>
command line option
--db_refseq_plant
command line option
--db_taxonomy_16S
command line option
--db_taxonomy_ITS
command line option
--ins_len <insert_length>
command line option
-16S
command line option
-e
command line option
-h, --help
command line option
-humann
command line option
-ic <method>, --initial_cleaning <method>
command line option
-ITS
command line option
-m <mode>, --mode <mode>
command line option
-MV <parameters>
command line option
-o <output_directory>, --out_dir <output_directory>
command line option
-ot <output_type_list>, --output_type <output_type_list>
command line option
-postfix <postfix>
command line option
-r <root_directory>, --root_dir <root_directory>
command line option
-rapsearch <database>
command line option
-reconstruct <option>
command line option
-refseq <kingdom>
command line option
-t <threads>, --threads <threads>
command line option
A
adapter_read() (in module refseq_bipype)
adapter_read_bck() (in module refseq_bipype)
auto_tax_read() (in module metatranscriptomics_bipype)
(in module refseq_bipype)
B
bam_idxstating() (in module refseq_bipype)
bam_indexing() (in module refseq_bipype)
bam_make() (in module refseq_bipype)
bam_sorting() (in module refseq_bipype)
bipype (module)
bowtie2_run() (in module refseq_bipype)
C
cat_read() (in module refseq_bipype)
command line option
--cutadapt <adapter_file> <search_options>
--db_16S <database>
--db_ITS <database>
--db_NCBI_taxonomy
--db_reconstruct
--db_refseq_fungi <databases>
--db_refseq_plant
--db_taxonomy_16S
--db_taxonomy_ITS
--ins_len <insert_length>
-16S
-ITS
-MV <parameters>
-e
-h, --help
-humann
-ic <method>, --initial_cleaning <method>
-m <mode>, --mode <mode>
-o <output_directory>, --out_dir <output_directory>
-ot <output_type_list>, --output_type <output_type_list>
-postfix <postfix>
-r <root_directory>, --root_dir <root_directory>
-rapsearch <database>
-reconstruct <option>
-refseq <kingdom>
-t <threads>, --threads <threads>
config_from_file() (in module metatranscriptomics_bipype)
connect_db() (in module metatranscriptomics_bipype)
create_krona_html() (in module refseq_bipype)
create_krona_xml() (in module refseq_bipype)
cutadapt() (in module refseq_bipype)
D
deunique() (in module refseq_bipype)
dict_prepare() (in module refseq_bipype)
dict_purify() (in module refseq_bipype)
dict_sum() (in module refseq_bipype)
dicto_reduce() (in module metatranscriptomics_bipype)
E
exist_check() (in module refseq_bipype)
F
fastq_dict() (in module refseq_bipype)
fastq_to_fasta() (in module metatranscriptomics_bipype)
file_analysis() (in module refseq_bipype)
G
get_kegg_name() (in module metatranscriptomics_bipype)
get_ko_fc() (in module metatranscriptomics_bipype)
get_kopathways() (in module metatranscriptomics_bipype)
get_pathways() (in module metatranscriptomics_bipype)
get_tables() (in module metatranscriptomics_bipype)
graphlan_to_krona() (in module refseq_bipype)
gzip_MV() (in module refseq_bipype)
H
humann() (in module refseq_bipype)
I
idx_map() (in module refseq_bipype)
idx_reader() (in module refseq_bipype)
idxstat_perling() (in module refseq_bipype)
input_locations() (in module refseq_bipype)
ins_len_read() (in module refseq_bipype)
L
linia_unique() (in module refseq_bipype)
low_change() (in module metatranscriptomics_bipype)
M
m8_to_ko() (in module metatranscriptomics_bipype)
mapper() (in module metatranscriptomics_bipype)
mapper_write() (in module metatranscriptomics_bipype)
metatranscriptomics() (in module metatranscriptomics_bipype)
metatranscriptomics_bipype (module)
MH() (in module refseq_bipype)
MV() (in module refseq_bipype)
N
name_total_reduction() (in module refseq_bipype)
O
out_content() (in module metatranscriptomics_bipype)
out_namespace() (in module refseq_bipype)
P
pair_uni_name() (in module refseq_bipype)
paired_end_match() (in module refseq_bipype)
parse_arguments() (in module bipype)
pickle_or_db() (in module metatranscriptomics_bipype)
prepare_taxonomy_dicts() (in module refseq_bipype)
prepare_taxonomy_stats() (in module refseq_bipype)
prettify() (in module refseq_bipype)
progress() (in module metatranscriptomics_bipype)
R
rapsearch() (in module refseq_bipype)
rapsearch2() (in module metatranscriptomics_bipype)
reconstruct() (in module refseq_bipype)
refseq_bipype (module)
refseq_mapping() (in module refseq_bipype)
refseq_ref_namespace() (in module refseq_bipype)
run_cat_pairing() (in module metatranscriptomics_bipype)
run_fastq_to_fasta() (in module metatranscriptomics_bipype)
run_ko_csv() (in module metatranscriptomics_bipype)
run_ko_map() (in module metatranscriptomics_bipype)
run_ko_remap() (in module metatranscriptomics_bipype)
run_megan() (in module refseq_bipype)
run_new_ko_remap() (in module metatranscriptomics_bipype)
run_pre_ko_remap() (in module metatranscriptomics_bipype)
run_rapsearch() (in module metatranscriptomics_bipype)
run_SARTools() (in module metatranscriptomics_bipype)
S
sam_merge() (in module refseq_bipype)
sample() (in module refseq_bipype)
SSU_read() (in module refseq_bipype)
T
tax_id_reader() (in module refseq_bipype)
tax_name_reader() (in module refseq_bipype)
tax_tree_extend() (in module refseq_bipype)
tax_tree_graphlan() (in module refseq_bipype)
taxa_read() (in module refseq_bipype)
tree_of_life() (in module refseq_bipype)
tuple_to_dict() (in module refseq_bipype)
tuple_to_xml_dict() (in module refseq_bipype)
txt_dict_clean() (in module refseq_bipype)
U
update_dict() (in module refseq_bipype)
usearch() (in module refseq_bipype)
X
xml_counts_graphlan() (in module refseq_bipype)
xml_format() (in module refseq_bipype)
xml_name_parse() (in module refseq_bipype)
xml_names_graphlan() (in module refseq_bipype)
xml_prepare() (in module refseq_bipype)
xml_vals() (in module refseq_bipype)
Read the Docs
v: latest
Versions
latest
Downloads
pdf
htmlzip
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.