Genestack Python Client Library
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Genestack Python Client Library
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Index
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C
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W
A
ActualOwnerFileFilter (class in genestack_client.file_filters)
ActualPermissionFileFilter (class in genestack_client.file_filters)
add_boolean() (genestack_client.Metainfo method)
add_checksums() (genestack_client.FilesUtil method)
add_dataset_children() (genestack_client.DatasetsUtil method)
add_date_time() (genestack_client.Metainfo method)
add_decimal() (genestack_client.Metainfo method)
add_external_link() (genestack_client.Metainfo method)
add_file_reference() (genestack_client.Metainfo method)
add_file_to_datasets() (genestack_client.DatasetsUtil method)
add_filter() (genestack_client.genome_query.GenomeQuery method)
add_integer() (genestack_client.Metainfo method)
add_memory_size() (genestack_client.Metainfo method)
add_metainfo_string_value() (genestack_client.FilesUtil method)
add_metainfo_values() (genestack_client.FilesUtil method)
add_organization() (genestack_client.Metainfo method)
add_person() (genestack_client.Metainfo method)
add_publication() (genestack_client.Metainfo method)
add_string() (genestack_client.Metainfo method)
add_temperature() (genestack_client.Metainfo method)
add_time() (genestack_client.Metainfo method)
add_value() (genestack_client.Metainfo method)
AFFYMETRIX_ANNOTATION (genestack_client.DataImporter attribute)
AffymetrixMicroarraysNormalizationApplication (class in genestack_client)
AGILENT_ANNOTATION (genestack_client.DataImporter attribute)
AgilentMicroarraysNormalizationApplication (class in genestack_client)
ALIGNED_READS (genestack_client.file_types.FileTypes attribute)
AlignedReadsQC (class in genestack_client)
AlignedReadsSubsamplingApplication (class in genestack_client)
AND() (genestack_client.file_filters.FileFilter method)
AndFileFilter (class in genestack_client.file_filters)
Application (class in genestack_client)
application() (genestack_client.Connection method)
APPLICATION_ID (genestack_client.AffymetrixMicroarraysNormalizationApplication attribute)
(genestack_client.AgilentMicroarraysNormalizationApplication attribute)
(genestack_client.AlignedReadsQC attribute)
(genestack_client.AlignedReadsSubsamplingApplication attribute)
(genestack_client.ArrayQualityMetricsApplication attribute)
(genestack_client.BWAApplication attribute)
(genestack_client.BowtieApplication attribute)
(genestack_client.BsmapApplication attribute)
(genestack_client.BsmapApplicationWG attribute)
(genestack_client.ConcatenateVariantsApplication attribute)
(genestack_client.CuffquantApplication attribute)
(genestack_client.DatasetsUtil attribute)
(genestack_client.DoseResponseApplication attribute)
(genestack_client.EffectPredictionApplication attribute)
(genestack_client.FastQCApplicaton attribute)
(genestack_client.FilterByQuality attribute)
(genestack_client.FilterDuplicatedReads attribute)
(genestack_client.GOEnrichmentAnalysis attribute)
(genestack_client.GenePixMicroarraysNormalizationApplication attribute)
(genestack_client.HTSeqCountsApplication attribute)
(genestack_client.InfiniumMicroarraysNormalizationApplication attribute)
(genestack_client.IntersectApplication attribute)
(genestack_client.IntersectGenomicFeaturesMapped attribute)
(genestack_client.IntersectGenomicFeaturesVariants attribute)
(genestack_client.L1000MicroarraysNormalizationApplication attribute)
(genestack_client.MarkDuplicated attribute)
(genestack_client.MergeMappedReadsApplication attribute)
(genestack_client.MethratioApplication attribute)
(genestack_client.NormalizationApplication attribute)
(genestack_client.QiimeMicrobiomeAnalysis attribute)
(genestack_client.RemoveDuplicated attribute)
(genestack_client.SingleCellRNASeqAnalysisApplication attribute)
(genestack_client.SingleCellRNASeqVisualiserApplication attribute)
(genestack_client.SubsampleReads attribute)
(genestack_client.TargetedSequencingQC attribute)
(genestack_client.TestCLApplication attribute)
(genestack_client.TophatApplication attribute)
(genestack_client.TrimAdaptorsAndContaminants attribute)
(genestack_client.TrimLowQualityBases attribute)
(genestack_client.TrimToFixedLength attribute)
(genestack_client.UnalignedReadsQC attribute)
(genestack_client.VariantsAssociationAnalysisApplication attribute)
(genestack_client.VariationCaller2Application attribute)
(genestack_client.VariationCallerApplication attribute)
(genestack_client.VariationMergerApplication attribute)
(genestack_client.expression_navigator.ExpressionNavigatorforGenes attribute)
(genestack_client.expression_navigator.ExpressionNavigatorforIsoforms attribute)
(genestack_client.expression_navigator.ExpressionNavigatorforMicroarrays attribute)
(genestack_client.samples.SampleLinker attribute)
APPLICATION_PAGE_FILE (genestack_client.file_types.FileTypes attribute)
ArrayQualityMetricsApplication (class in genestack_client)
AUXILIARY_FILE (genestack_client.file_types.FileTypes attribute)
B
BATCH_SIZE (genestack_client.DatasetsUtil attribute)
BelongsToDatasetFileFilter (class in genestack_client.file_filters)
BooleanValue (class in genestack_client.metainfo_scalar_values)
BowtieApplication (class in genestack_client)
BsmapApplication (class in genestack_client)
BsmapApplicationWG (class in genestack_client)
BTB_DOCUMENT (genestack_client.file_types.FileTypes attribute)
BWAApplication (class in genestack_client)
BY_FDR (genestack_client.genome_query.GenomeQuery.SortingOrder attribute)
BY_LOG_COUNTS (genestack_client.genome_query.GenomeQuery.SortingOrder attribute)
BY_LOG_FOLD_CHANGE (genestack_client.genome_query.GenomeQuery.SortingOrder attribute)
C
change_command_line_arguments() (genestack_client.CLApplication method)
check_version() (genestack_client.Connection method)
ChildrenFileFilter (class in genestack_client.file_filters)
CLApplication (class in genestack_client)
cmdloop() (genestack_client.genestack_shell.GenestackShell method)
CODON_TABLE (genestack_client.file_types.FileTypes attribute)
collect_initializable_files_in_container() (genestack_client.FilesUtil method)
collect_metainfos() (genestack_client.FilesUtil method)
Command (class in genestack_client.genestack_shell)
ConcatenateVariantsApplication (class in genestack_client)
Connection (class in genestack_client)
CONTAINER (genestack_client.file_types.FileTypes attribute)
ContainsFileFilter (class in genestack_client.file_filters)
count_file_children() (genestack_client.FilesUtil method)
create_bam() (genestack_client.DataImporter method)
create_bed() (genestack_client.DataImporter method)
create_dataset() (genestack_client.DatasetsUtil method)
create_dbnsfp() (genestack_client.DataImporter method)
create_dictionary() (genestack_client.DataImporter method)
create_empty_dataset() (genestack_client.DatasetsUtil method)
create_expression_levels() (genestack_client.DataImporter method)
create_file() (genestack_client.CLApplication method)
(genestack_client.IntersectApplication method)
(genestack_client.expression_navigator.ExpressionNavigatorforGenes method)
(genestack_client.expression_navigator.ExpressionNavigatorforIsoforms method)
(genestack_client.expression_navigator.ExpressionNavigatorforMicroarrays method)
create_folder() (genestack_client.FilesUtil method)
create_gene_expression_signature() (genestack_client.DataImporter method)
create_gene_list() (genestack_client.DataImporter method)
create_genome_annotation() (genestack_client.DataImporter method)
create_infinium_microarray_data() (genestack_client.DataImporter method)
create_mapped_reads_count() (genestack_client.DataImporter method)
create_microarray_annotation() (genestack_client.DataImporter method)
create_microarray_data() (genestack_client.DataImporter method)
create_reference_genome() (genestack_client.DataImporter method)
create_report_file() (genestack_client.DataImporter method)
create_subset() (genestack_client.DatasetsUtil method)
create_unaligned_read() (genestack_client.DataImporter method)
create_upload_dataset() (genestack_client.samples.SampleLinker method)
create_vcf() (genestack_client.DataImporter method)
create_wig() (genestack_client.DataImporter method)
CuffquantApplication (class in genestack_client)
D
DataImporter (class in genestack_client)
DATASET (genestack_client.file_types.FileTypes attribute)
DatasetsUtil (class in genestack_client)
DateTimeValue (class in genestack_client.metainfo_scalar_values)
DecimalValue (class in genestack_client.metainfo_scalar_values)
default() (genestack_client.genestack_shell.GenestackShell method)
DICTIONARY_FILE (genestack_client.file_types.FileTypes attribute)
DIFFERENTIAL_EXPRESSION_FILE (genestack_client.file_types.FileTypes attribute)
do_help() (genestack_client.genestack_shell.GenestackShell method)
DoseResponseApplication (class in genestack_client)
DOWN (genestack_client.genome_query.GenomeQuery.Regulation attribute)
E
EDIT (genestack_client.ShareUtil.Permissions attribute)
EffectPredictionApplication (class in genestack_client)
emptyline() (genestack_client.genestack_shell.GenestackShell method)
EXPRESSION_LEVELS (genestack_client.file_types.FileTypes attribute)
ExpressionNavigatorforGenes (class in genestack_client.expression_navigator)
ExpressionNavigatorforIsoforms (class in genestack_client.expression_navigator)
ExpressionNavigatorforMicroarrays (class in genestack_client.expression_navigator)
EXTERNAL_DATABASE (genestack_client.file_types.FileTypes attribute)
ExternalLink (class in genestack_client.metainfo_scalar_values)
F
FastQCApplicaton (class in genestack_client)
FEATURE_LIST (genestack_client.file_types.FileTypes attribute)
FILE (genestack_client.file_types.FileTypes attribute)
FILE_ACCESS (genestack_client.file_permissions.Permissions attribute)
FILE_CLONE_DATA (genestack_client.file_permissions.Permissions attribute)
FILE_READ_CONTENT (genestack_client.file_permissions.Permissions attribute)
FILE_WRITE (genestack_client.file_permissions.Permissions attribute)
FileFilter (class in genestack_client.file_filters)
FileInitializer (class in genestack_client)
FileReference (class in genestack_client.metainfo_scalar_values)
FilesUtil (class in genestack_client)
FileTypes (class in genestack_client.file_types)
FilterByQuality (class in genestack_client)
FilterDuplicatedReads (class in genestack_client)
find_file_by_name() (genestack_client.FilesUtil method)
find_files() (genestack_client.FilesUtil method)
find_group_by_name() (genestack_client.GroupsUtil method)
find_or_create_folder() (genestack_client.FilesUtil method)
find_reference_genome() (genestack_client.FilesUtil method)
FixedValueFileFilter (class in genestack_client.file_filters)
FOLDER (genestack_client.file_types.FileTypes attribute)
G
GENE_EXPRESSION_SIGNATURE (genestack_client.file_types.FileTypes attribute)
GenePixMicroarraysNormalizationApplication (class in genestack_client)
genestack_client.expression_navigator (module)
genestack_client.file_filters (module)
genestack_client.metainfo_scalar_values (module)
GenestackAuthenticationException (class in genestack_client)
GenestackBaseException (class in genestack_client)
GenestackConnectionFailure (class in genestack_client)
GenestackException (class in genestack_client)
GenestackResponseError (class in genestack_client)
GenestackServerException (class in genestack_client)
GenestackShell (class in genestack_client.genestack_shell)
GENOME_ANNOTATIONS (genestack_client.file_types.FileTypes attribute)
GENOME_BED_DATA (genestack_client.file_types.FileTypes attribute)
GENOME_WIGGLE_DATA (genestack_client.file_types.FileTypes attribute)
GenomeQuery (class in genestack_client.genome_query)
GenomeQuery.Filter (class in genestack_client.genome_query)
GenomeQuery.Regulation (class in genestack_client.genome_query)
GenomeQuery.SortingOrder (class in genestack_client.genome_query)
get_accession() (genestack_client.metainfo_scalar_values.FileReference method)
get_available_sharing_groups() (genestack_client.ShareUtil method)
get_boolean() (genestack_client.metainfo_scalar_values.BooleanValue method)
get_command_parser() (genestack_client.genestack_shell.Command method)
get_commands_for_help() (genestack_client.genestack_shell.GenestackShell method)
get_connection() (genestack_client.settings.User method)
(in module genestack_client)
get_dataset_children() (genestack_client.DatasetsUtil method)
get_dataset_size() (genestack_client.DatasetsUtil method)
get_date() (genestack_client.metainfo_scalar_values.DateTimeValue method)
get_decimal() (genestack_client.metainfo_scalar_values.DecimalValue method)
get_file_children() (genestack_client.FilesUtil method)
get_folder() (genestack_client.FilesUtil method)
get_format() (genestack_client.metainfo_scalar_values.ExternalLink method)
get_history_file_path() (genestack_client.genestack_shell.GenestackShell method)
get_home_folder() (genestack_client.FilesUtil method)
get_infos() (genestack_client.FilesUtil method)
get_int() (genestack_client.metainfo_scalar_values.IntegerValue method)
(genestack_client.metainfo_scalar_values.MemorySizeValue method)
get_map() (genestack_client.genome_query.GenomeQuery method)
get_metainfo_values_as_string_list() (genestack_client.FilesUtil method)
get_metainfo_values_as_strings() (genestack_client.FilesUtil method)
get_milliseconds() (genestack_client.metainfo_scalar_values.DateTimeValue method)
get_organization() (genestack_client.metainfo_scalar_values.Organization method)
get_person() (genestack_client.metainfo_scalar_values.Person method)
get_public_folder() (genestack_client.FilesUtil method)
get_publication() (genestack_client.metainfo_scalar_values.Publication method)
get_response() (genestack_client.Application method)
get_shell_parser() (genestack_client.genestack_shell.GenestackShell method)
get_short_description() (genestack_client.genestack_shell.Command method)
get_special_folder() (genestack_client.FilesUtil method)
get_string() (genestack_client.metainfo_scalar_values.StringValue method)
get_text() (genestack_client.metainfo_scalar_values.ExternalLink method)
get_url() (genestack_client.metainfo_scalar_values.ExternalLink method)
get_user() (in module genestack_client)
GOEnrichmentAnalysis (class in genestack_client)
GroupsUtil (class in genestack_client)
H
HasInProvenanceFileFilter (class in genestack_client.file_filters)
HT_SEQ_COUNTS (genestack_client.file_types.FileTypes attribute)
HTSeqCountsApplication (class in genestack_client)
I
import_data() (genestack_client.samples.SampleLinker method)
INDEX_FILE (genestack_client.file_types.FileTypes attribute)
INFINIUM_ANNOTATION (genestack_client.DataImporter attribute)
InfiniumMicroarraysNormalizationApplication (class in genestack_client)
initialize() (genestack_client.FileInitializer method)
IntegerValue (class in genestack_client.metainfo_scalar_values)
IntersectApplication (class in genestack_client)
IntersectGenomicFeaturesMapped (class in genestack_client)
IntersectGenomicFeaturesVariants (class in genestack_client)
invoke() (genestack_client.Application method)
K
KeyValueFileFilter (class in genestack_client.file_filters)
L
L1000MicroarraysNormalizationApplication (class in genestack_client)
link_file() (genestack_client.FilesUtil method)
link_files() (genestack_client.FilesUtil method)
load_info() (genestack_client.FileInitializer method)
load_raw() (genestack_client.DataImporter method)
login() (genestack_client.Connection method)
login_by_token() (genestack_client.Connection method)
logout() (genestack_client.Connection method)
M
make_connection_parser() (in module genestack_client)
mark_for_tests() (genestack_client.FilesUtil method)
mark_obsolete() (genestack_client.FilesUtil method)
MarkDuplicated (class in genestack_client)
MAX_FDR (genestack_client.genome_query.GenomeQuery.Filter attribute)
MemorySizeValue (class in genestack_client.metainfo_scalar_values)
merge_datasets() (genestack_client.DatasetsUtil method)
MergeMappedReadsApplication (class in genestack_client)
Metainfo (class in genestack_client)
MetainfoScalarValue (class in genestack_client.metainfo_scalar_values)
MetainfoValuePatternFileFilter (class in genestack_client.file_filters)
MethratioApplication (class in genestack_client)
MICROARRAY_ANNOTATION_TYPES (genestack_client.DataImporter attribute)
MICROARRAY_DATA (genestack_client.file_types.FileTypes attribute)
MIN_LOG_COUNTS (genestack_client.genome_query.GenomeQuery.Filter attribute)
MIN_LOG_FOLD_CHANGE (genestack_client.genome_query.GenomeQuery.Filter attribute)
N
NormalizationApplication (class in genestack_client)
NotFileFilter (class in genestack_client.file_filters)
O
OR() (genestack_client.file_filters.FileFilter method)
OrFileFilter (class in genestack_client.file_filters)
Organization (class in genestack_client.metainfo_scalar_values)
OwnerFileFilter (class in genestack_client.file_filters)
P
parse_metainfo_from_dict() (genestack_client.Metainfo class method)
perform_request() (genestack_client.Connection method)
PermissionFileFilter (class in genestack_client.file_filters)
Permissions (class in genestack_client.file_permissions)
Person (class in genestack_client.metainfo_scalar_values)
PKG_DESEQ (genestack_client.expression_navigator.ExpressionNavigatorforGenes attribute)
PKG_EDGER (genestack_client.expression_navigator.ExpressionNavigatorforGenes attribute)
postloop() (genestack_client.genestack_shell.GenestackShell method)
PREFERENCES_FILE (genestack_client.file_types.FileTypes attribute)
preloop() (genestack_client.genestack_shell.GenestackShell method)
print_log() (genestack_client.TaskLogViewer method)
process_command() (genestack_client.genestack_shell.GenestackShell method)
Publication (class in genestack_client.metainfo_scalar_values)
Q
QiimeMicrobiomeAnalysis (class in genestack_client)
R
RAW_FILE (genestack_client.file_types.FileTypes attribute)
REFERENCE_GENOME (genestack_client.file_types.FileTypes attribute)
REGULATION (genestack_client.genome_query.GenomeQuery.Filter attribute)
release() (genestack_client.samples.SampleLinker method)
remove_dataset_children() (genestack_client.DatasetsUtil method)
remove_metainfo_value() (genestack_client.FilesUtil method)
RemoveDuplicated (class in genestack_client)
rename_file() (genestack_client.FilesUtil method)
replace_file_reference() (genestack_client.CLApplication method)
replace_metainfo_string_value() (genestack_client.FilesUtil method)
replace_metainfo_value() (genestack_client.FilesUtil method)
REPORT_FILE (genestack_client.file_types.FileTypes attribute)
run() (genestack_client.genestack_shell.Command method)
S
safe_share_files() (genestack_client.ShareUtil method)
SAMPLE (genestack_client.file_types.FileTypes attribute)
SampleLinker (class in genestack_client.samples)
SEARCH_FOLDER (genestack_client.file_types.FileTypes attribute)
set_arguments() (genestack_client.genestack_shell.Command method)
set_connection() (genestack_client.genestack_shell.Command method)
set_contrasts() (genestack_client.genome_query.GenomeQuery method)
set_feature_ids() (genestack_client.genome_query.GenomeQuery method)
set_limit() (genestack_client.genome_query.GenomeQuery method)
set_offset() (genestack_client.genome_query.GenomeQuery method)
set_order_ascending() (genestack_client.genome_query.GenomeQuery method)
set_shell_user() (genestack_client.genestack_shell.GenestackShell method)
set_sorting_order() (genestack_client.genome_query.GenomeQuery method)
SHARE (genestack_client.ShareUtil.Permissions attribute)
share_files() (genestack_client.ShareUtil method)
share_files_for_edit() (genestack_client.ShareUtil method)
share_files_for_view() (genestack_client.ShareUtil method)
share_folder() (genestack_client.ShareUtil method)
ShareUtil (class in genestack_client)
ShareUtil.Permissions (class in genestack_client)
SingleCellRNASeqAnalysisApplication (class in genestack_client)
SingleCellRNASeqVisualiserApplication (class in genestack_client)
SpecialFolders (class in genestack_client)
start() (genestack_client.CLApplication method)
StringValue (class in genestack_client.metainfo_scalar_values)
SubsampleReads (class in genestack_client)
T
TargetedSequencingQC (class in genestack_client)
TaskLogViewer (class in genestack_client)
TestCLApplication (class in genestack_client)
TophatApplication (class in genestack_client)
TrimAdaptorsAndContaminants (class in genestack_client)
TrimLowQualityBases (class in genestack_client)
TrimToFixedLength (class in genestack_client)
TSV_ANNOTATION (genestack_client.DataImporter attribute)
TypeFileFilter (class in genestack_client.file_filters)
U
UNALIGNED_READS (genestack_client.file_types.FileTypes attribute)
UnalignedReadsQC (class in genestack_client)
unlink_data() (genestack_client.samples.SampleLinker method)
unlink_file() (genestack_client.FilesUtil method)
unlink_files() (genestack_client.FilesUtil method)
UP (genestack_client.genome_query.GenomeQuery.Regulation attribute)
update_parser() (genestack_client.genestack_shell.Command method)
upload_file() (genestack_client.Application method)
User (class in genestack_client.settings)
V
VariantsAssociationAnalysisApplication (class in genestack_client)
VARIATION_FILE (genestack_client.file_types.FileTypes attribute)
VariationCaller2Application (class in genestack_client)
VariationCallerApplication (class in genestack_client)
VariationMergerApplication (class in genestack_client)
VIEW (genestack_client.ShareUtil.Permissions attribute)
W
whoami() (genestack_client.Connection method)
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