pyrpipe
latest
Installation
Tutorial
Cookbook
pyrpipe
Docs
»
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
P
|
Q
|
R
|
S
|
T
|
V
|
W
|
Y
A
add_bool() (in module pyrpipe.param_loader)
align() (pyrpipe.sra.SRA method)
Aligner (class in pyrpipe.mapping)
assemble() (pyrpipe.sra.SRA method)
Assembly (class in pyrpipe.assembly)
B
BBmap (class in pyrpipe.qc)
Benchmark (class in pyrpipe.benchmark)
Bowtie2 (class in pyrpipe.mapping)
build_index() (pyrpipe.mapping.Aligner method)
(pyrpipe.mapping.Bowtie2 method)
(pyrpipe.mapping.Hisat2 method)
(pyrpipe.mapping.Star method)
(pyrpipe.quant.Kallisto method)
(pyrpipe.quant.Quant method)
(pyrpipe.quant.Salmon method)
build_tools() (in module pyrpipe.buildtools)
byte_to_readable() (in module pyrpipe.pyrpipe_utils)
C
check_bowtie2index() (in module pyrpipe.pyrpipe_utils)
check_dependencies() (in module pyrpipe.pyrpipe_engine)
check_dependency() (pyrpipe.runnable.Runnable method)
check_files_exist() (in module pyrpipe.pyrpipe_utils)
check_hisatindex() (in module pyrpipe.pyrpipe_utils)
check_index() (pyrpipe.mapping.Aligner method)
(pyrpipe.mapping.Bowtie2 method)
(pyrpipe.mapping.Hisat2 method)
(pyrpipe.mapping.Star method)
(pyrpipe.quant.Kallisto method)
(pyrpipe.quant.Quant method)
(pyrpipe.quant.Salmon method)
check_kallistoindex() (in module pyrpipe.pyrpipe_utils)
check_paths_exist() (in module pyrpipe.pyrpipe_utils)
check_salmonindex() (in module pyrpipe.pyrpipe_utils)
check_starindex() (in module pyrpipe.pyrpipe_utils)
checkEnvLog() (in module pyrpipe.reports)
Conf (class in pyrpipe)
create_lock() (pyrpipe.runnable.Runnable method)
create_logger() (pyrpipe.PyrpipeLogger method)
Cufflinks (class in pyrpipe.assembly)
D
delete_fastq() (pyrpipe.sra.SRA method)
delete_file() (in module pyrpipe.pyrpipe_engine)
delete_files() (in module pyrpipe.pyrpipe_engine)
delete_sra() (pyrpipe.sra.SRA method)
download_fastq() (pyrpipe.sra.SRA method)
download_sra() (pyrpipe.sra.SRA method)
dryable() (in module pyrpipe.pyrpipe_engine)
E
execute_command() (in module pyrpipe.pyrpipe_engine)
execute_commandRealtime() (in module pyrpipe.pyrpipe_engine)
F
fastq_exists() (pyrpipe.sra.SRA method)
find_files() (in module pyrpipe.pyrpipe_utils)
format() (pyrpipe.LogFormatter method)
G
generate_multiqc() (in module pyrpipe.reports)
generate_multiqc_from_log() (in module pyrpipe.reports)
generate_summary() (in module pyrpipe.reports)
generateBashScript() (in module pyrpipe.reports)
generateBenchmarkReport() (in module pyrpipe.reports)
generateEnvReportTable() (in module pyrpipe.reports)
generateHTMLReport() (in module pyrpipe.reports)
get_file_basename() (in module pyrpipe.pyrpipe_utils)
get_file_directory() (in module pyrpipe.pyrpipe_utils)
get_file_size() (in module pyrpipe.pyrpipe_utils)
get_fileext() (in module pyrpipe.pyrpipe_utils)
get_filename() (in module pyrpipe.pyrpipe_utils)
get_kwargs() (pyrpipe.param_loader.YAML_loader method)
get_lock_files() (pyrpipe.runnable.Runnable method)
get_mdf() (in module pyrpipe.pyrpipe_utils)
get_params() (pyrpipe.param_loader.YAML_loader method)
get_program_path() (in module pyrpipe.pyrpipe_engine)
get_program_version() (in module pyrpipe.pyrpipe_engine)
get_programtime_boxdata() (pyrpipe.benchmark.Benchmark method)
get_read_length() (pyrpipe.sra.SRA method)
get_return_status() (in module pyrpipe.pyrpipe_engine)
get_shell_output() (in module pyrpipe.pyrpipe_engine)
get_time_perobject() (pyrpipe.benchmark.Benchmark method)
get_time_perprogram() (pyrpipe.benchmark.Benchmark method)
get_timestamp() (in module pyrpipe.pyrpipe_utils)
get_union() (in module pyrpipe.pyrpipe_utils)
get_valid_parameters() (pyrpipe.runnable.Runnable method)
getCommandsFromLog() (in module pyrpipe.reports)
getStdoutFromLog() (in module pyrpipe.reports)
getTimestamp() (in module pyrpipe.pyrpipe_session)
goodbye() (in module pyrpipe)
H
Hisat2 (class in pyrpipe.mapping)
I
init_cmdlog() (pyrpipe.PyrpipeLogger method)
init_envlog() (pyrpipe.PyrpipeLogger method)
init_from_accession() (pyrpipe.sra.SRA method)
init_object() (pyrpipe.sra.SRA method)
init_sys_args() (pyrpipe.Conf method)
init_threads_mem() (pyrpipe.Conf method)
is_paired() (in module pyrpipe.pyrpipe_engine)
K
Kallisto (class in pyrpipe.quant)
L
load_args() (pyrpipe.runnable.Runnable method)
load_yaml() (pyrpipe.runnable.Runnable method)
LogFormatter (class in pyrpipe)
M
merge_bam() (pyrpipe.tools.Samtools method)
mkdir() (in module pyrpipe.pyrpipe_utils)
move_file() (in module pyrpipe.pyrpipe_engine)
P
parse_cmd() (in module pyrpipe.pyrpipe_engine)
parse_java_args() (in module pyrpipe.pyrpipe_utils)
parse_logs() (pyrpipe.benchmark.Benchmark method)
parse_params() (pyrpipe.param_loader.YAML_loader method)
parse_runtime() (pyrpipe.benchmark.Benchmark method)
parse_unix_args() (in module pyrpipe.pyrpipe_utils)
parseEnvLog() (in module pyrpipe.reports)
perform_alignment() (pyrpipe.mapping.Aligner method)
(pyrpipe.mapping.Bowtie2 method)
(pyrpipe.mapping.Hisat2 method)
(pyrpipe.mapping.Star method)
perform_assembly() (pyrpipe.assembly.Assembly method)
(pyrpipe.assembly.Cufflinks method)
(pyrpipe.assembly.Stringtie method)
perform_cleaning() (pyrpipe.qc.BBmap method)
perform_qc() (pyrpipe.qc.BBmap method)
(pyrpipe.qc.RNASeqQC method)
(pyrpipe.qc.Trimgalore method)
perform_quant() (pyrpipe.quant.Kallisto method)
(pyrpipe.quant.Quant method)
(pyrpipe.quant.Salmon method)
plot_time_perobject() (pyrpipe.benchmark.Benchmark method)
plot_time_perprogram() (pyrpipe.benchmark.Benchmark method)
print_blue() (in module pyrpipe.pyrpipe_utils)
print_boldred() (in module pyrpipe.pyrpipe_utils)
print_error() (in module pyrpipe.pyrpipe_utils)
print_green() (in module pyrpipe.pyrpipe_utils)
print_message() (in module pyrpipe.pyrpipe_utils)
print_notification() (in module pyrpipe.pyrpipe_utils)
print_success() (in module pyrpipe.pyrpipe_utils)
print_warning() (in module pyrpipe.pyrpipe_utils)
print_yellow() (in module pyrpipe.pyrpipe_utils)
pyrpipe (module)
pyrpipe.arg_parser (module)
pyrpipe.assembly (module)
pyrpipe.benchmark (module)
pyrpipe.buildtools (module)
pyrpipe.mapping (module)
pyrpipe.param_loader (module)
pyrpipe.pyrpipe_engine (module)
pyrpipe.pyrpipe_session (module)
pyrpipe.pyrpipe_utils (module)
pyrpipe.qc (module)
pyrpipe.quant (module)
pyrpipe.report_templates (module)
pyrpipe.reports (module)
pyrpipe.runnable (module)
pyrpipe.sra (module)
pyrpipe.test_sratools (module)
pyrpipe.tools (module)
pyrpipe.valid_args (module)
pyrpipe.version (module)
pyrpipe_print() (in module pyrpipe.pyrpipe_utils)
PyrpipeLogger (class in pyrpipe)
Q
Quant (class in pyrpipe.quant)
quant() (pyrpipe.sra.SRA method)
R
remove_locks() (pyrpipe.runnable.Runnable method)
resolve_parameter() (pyrpipe.runnable.Runnable method)
restore_session() (in module pyrpipe.pyrpipe_session)
RNASeqQC (class in pyrpipe.qc)
RNASeqTools (class in pyrpipe.tools)
run() (pyrpipe.runnable.Runnable method)
run_bbsplit() (pyrpipe.qc.BBmap method)
Runnable (class in pyrpipe.runnable)
runtest() (in module pyrpipe.test_sratools)
S
Salmon (class in pyrpipe.quant)
sam_sorted_bam() (pyrpipe.tools.Samtools method)
sam_to_bam() (pyrpipe.tools.Samtools method)
Samtools (class in pyrpipe.tools)
save_session() (in module pyrpipe.pyrpipe_session)
search_fastq() (pyrpipe.sra.SRA method)
skippable() (in module pyrpipe.pyrpipe_engine)
sort_bam() (pyrpipe.tools.Samtools method)
SRA (class in pyrpipe.sra)
sra_exists() (pyrpipe.sra.SRA method)
Star (class in pyrpipe.mapping)
Stringtie (class in pyrpipe.assembly)
T
trim() (pyrpipe.sra.SRA method)
Trimgalore (class in pyrpipe.qc)
V
verify_integrity() (pyrpipe.runnable.Runnable method)
verify_target() (pyrpipe.runnable.Runnable method)
verify_target_list() (pyrpipe.runnable.Runnable method)
W
writeHtml() (in module pyrpipe.reports)
writeHtmlToMarkdown() (in module pyrpipe.reports)
writeHtmlToPdf() (in module pyrpipe.reports)
Y
YAML_loader (class in pyrpipe.param_loader)
Read the Docs
v: latest
Versions
latest
stable
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.