Option	Mac-Displayed option	PC-Displayed option	PC-Displayed option2	Linux-Displayed option	Display object	Group	Notes	Descriptions	Global defaults	exon	AltMouse	gene	3'array	junction	RNASeq
dbase_version	"""Select database version """	"""Select database version  """	"""Select database version  """	"""Select database version  """	drop-down	ArrayType									
manufacturer_selection	"""Select vendor/data type """	"""Select vendor/data type  """	"""Select vendor/data type """	"""Select vendor or data type    """	drop-down	ArrayType									
species	"""Select species                """	"""Select species                   """	"""Select species                  """	"""Select species                      """	drop-down	ArrayType									
array_type	"""Select platform              """	"""Select platform                 """	"""Select platform               """	"""Select platform type             """	drop-down	ArrayType				---	---	---	---	---	---
update_dbs	"""Get new species/vendor/array databases online         """	"""Get new species/vendor/array databases online         """	"""Get new species/vendor/array databases online         """	"""Get new species/vendor/array databases online         """	single-checkbox	ArrayType				---	---	---	---	---	---
run_from_scratch	"""Analysis options          """	"""Analysis options          """	"""Analysis options          """	"""Analysis options          """	button	AnalysisType				Process CEL files|Process Expression file|Process AltAnalyze filtered|Annotate External Results|Additional Analyses	Process CEL files|Process Expression file|Process AltAnalyze filtered|Additional Analyses	Process CEL files|Process Expression file|Process AltAnalyze filtered|Annotate External Results|Additional Analyses	Process CEL files|Process Expression file|Additional Analyses	Process CEL files|Process Expression file|Process AltAnalyze filtered|Additional Analyses	Process RNA-seq reads|Process Expression file|Process AltAnalyze filtered|Additional Analyses
selected_version	"""Select database version  """	"""Select database version  """	"""Select database version  """	"""Select database version  """	comboBox	OnlineDatabases				---	---	---	---	---	---
selected_species1	"""Select species      """	"""Select species      """	"""Select species      """	"""Select species      """	comboBox	OnlineDatabases				---	---	---	---	---	---
selected_species2	"""Select species      """	"""Select species      """	"""Select species      """	"""Select species      """	comboBox	OnlineDatabases				---	---	---	---	---	---
selected_species3	"""Select species      """	"""Select species      """	"""Select species      """	"""Select species      """	comboBox	OnlineDatabases				---	---	---	---	---	---
additional_analyses	"""Additional options           """	"""Additional options           """	"""Additional options           """	"""Additional options           """	button	Additional Analyses				Pathway Enrichment|Pathway Visualization|Hierarchical Clustering|Principal Components|Lineage Analysis	Pathway Enrichment|Pathway Visualization|Hierarchical Clustering|Principal Components|Lineage Analysis	Pathway Enrichment|Pathway Visualization|Hierarchical Clustering|Principal Components|Lineage Analysis	Pathway Enrichment|Pathway Visualization|Hierarchical Clustering|Principal Components|Lineage Analysis	Pathway Enrichment|Pathway Visualization|Hierarchical Clustering|Principal Components|Lineage Analysis	Pathway Enrichment|Pathway Visualization|Hierarchical Clustering|Principal Components|Lineage Analysis
criterion_input_folder	Select GO-Elite Input file directory	Select GO-Elite Input file directory	Select GO-Elite Input file directory	Select GO-Elite Input file directory	folder	InputGOEliteDirs				---	---	---	---	---	---
criterion_denom_folder	Select GO-Elite Denominator file directory	Select GO-Elite Denominator file directory	Select GO-Elite Denominator file directory	Select GO-Elite Denominator file directory	folder	InputGOEliteDirs				---	---	---	---	---	---
main_output_folder	Select GO-Elite output directory	Select GO-Elite output directory	Select GO-Elite output directory	Select GO-Elite output directory	folder	InputGOEliteDirs	"note: by default, the output will be stored in a set of new directories under\kthe same directory as the input ID folder."			---	---	---	---	---	---
new_run	Additional Options	Additional Options	Additional Options	Additional Options	button	AdditionalOptions				Perform GO/Pathway Analysis on Results|Change Parameters and Re-Run	Perform GO/Pathway Analysis on Results|Change Parameters and Re-Run	Perform GO/Pathway Analysis on Results|Change Parameters and Re-Run	Perform GO/Pathway Analysis on Results|Change Parameters and Re-Run	Perform GO/Pathway Analysis on Results|Change Parameters and Re-Run	Perform GO/Pathway Analysis on Results|Change Parameters and Re-Run
dataset_name	Give a name to this dataset	Give a name to this dataset	Give a name to this dataset	Give a name to this dataset	enter	InputCELFiles				---	---	---	---	---	---
input_cel_dir	Select the CEL file containing folder (required)	Select the CEL file containing folder (required)	Select the CEL file containing folder (required)	Select the CEL file containing folder (required)	folder	InputCELFiles				---	---	---	---	---	---
output_CEL_dir	Select an AltAnalyze result output directory	Select an AltAnalyze result output directory	Select an AltAnalyze result output directory	Select an AltAnalyze result output directory	folder	InputCELFiles				---	---	---	---	---	---
build_exon_bedfile	Build exon coordinate bed file to obtain BAM file exon counts	Build exon coordinate bed file to obtain BAM file exon counts	Build exon coordinate bed file to obtain BAM file exon counts	Build exon coordinate bed file to obtain BAM file exon counts	single-checkbox	InputCELFiles				NA	NA	NA	NA	NA	---
remove_xhyb	Remove probesets that have large cross-hybridization scores 	Remove probesets that have large cross-hybridization scores 	Remove probesets that have large cross-hybridization scores 	Remove probesets that have large cross-hybridization scores 	single-checkbox	InputCELFiles				---	---	NA	NA	NA	NA
input_cdf_file	Select the PGF library file for your array (required)	Select the PGF library file for your array (required)	Select the PGF library file for your array (required)	Select the PGF library file for your array (required)	file	InputLibraryFiles	note: the PGF file is apart of the standard library files for this array. This\kdirectory needs to also contain the CLF and BGP files for the array. These\kfiles can be downloaded from the Affymetrix website.			---	---	---	---	---	---
input_annotation_file	Select the CSV NetAffx annotation file for your array (recommended)	Select the CSV NetAffx annotation file for your array (recommended)	Select the CSV NetAffx annotation file for your array (recommended)	Select the CSV NetAffx annotation file for your array (recommended)	file	InputLibraryFiles	"note: the CSV annotation file should be listed under ""Current NetAffx\kannotations"" for this array."			---	---	---	---	---	---
input_exp_file	Select a probe set expression file (required)	Select a probe set expression file (required)	Select a probe set expression file (required)	Select a probe set expression file (required)	file	InputExpFiles				---	---	---	---	---	---
input_stats_file	Select a probe set p-value file (optional)	Select a probe set p-value file (optional)	Select a probe set p-value file (optional)	Select a probe set p-value file (optional)	file	InputExpFiles	"note: if not selected, an appropriate statistic file in the selected probe set\kexpression file directory will be used."			---	---	---	NA	---	---
output_dir	Select an AltAnalyze result output directory	Select an AltAnalyze result output directory	Select an AltAnalyze result output directory	Select an AltAnalyze result output directory	folder	InputExpFiles	"note: by default, the output will be stored in a set of new directories under\kthe same directory as the input expression file."			---	---	---	---	---	---
dabg_p	"""Remove probesets with a DABG p-value above   "" "	"""Remove probesets with a DABG p-value above   "" "	"""Remove probesets with a DABG p-value above   "" "	"""Remove probesets with a DABG p-value above   "" "	enter	GeneExpression		Maximum average DABG p-value (applied to one or both of the compared biological groups) for ExpressionBuilder filtering.		---	---	---	NA	---	NA
rpkm_threshold	"""Remove genes with an RPKM less than                """	"""Remove genes with an RPKM less than            """	"""Remove genes with an RPKM less than            """	"""Remove genes with an RPKM less than            """	enter	GeneExpression				NA	NA	NA	NA	NA	---
gene_exp_threshold	"""Remove genes expressed below (non-log)       ""   "	"""Remove exons expressed below (non-log)          ""   "	"""Remove exons expressed below (non-log)           ""  "	"""Remove exons expressed below (non-log)           ""  "	enter	GeneExpression		Maximum average non-log expression value (applied to one or both of the compared biological groups) for ExpressionBuilder filtering.		NA	NA	NA	NA	NA	---
exon_exp_threshold	"""Remove exons expressed below (non-log)       ""   "	"""Remove exons expressed below (non-log)          ""   "	"""Remove exons expressed below (non-log)           ""  "	"""Remove exons expressed below (non-log)           ""  "	enter	GeneExpression		Maximum average non-log expression value (applied to one or both of the compared biological groups) for ExpressionBuilder filtering.		NA	NA	NA	NA	NA	---
exon_rpkm_threshold	"""Remove exons with an RPKM less than                """	"""Remove exons with an RPKM less than            """	"""Remove exons with an RPKM less than            """	"""Remove exons with an RPKM less than            """	enter	GeneExpression				NA	NA	NA	NA	NA	---
expression_threshold	"""Remove probesets expressed below (non-log) ""   "	"""Remove probesets expressed below (non-log)    ""   "	"""Remove probesets expressed below (non-log) ""   "	"""Remove probesets expressed below (non-log) ""   "	enter	GeneExpression		Maximum average non-log expression value (applied to one or both of the compared biological groups) for ExpressionBuilder filtering.		---	---	---	NA	---	---
perform_alt_analysis	"""Perform alternative exon analysis                         """	"""Perform alternative exon analysis                         """	"""Perform alternative exon analysis                              """	"""Perform alternative exon analysis                        """	drop-down	GeneExpression		Indicates whether to just export the gene expression summary or in addition perform an alternative exon analysis.		yes|just expression	yes|just expression	yes|just expression	NA	yes|just expression	yes|just expression
analyze_as_groups	"""Organize samples into groups                              """	"""Organize samples into groups                                """	"""Organize samples into groups                                   """	"""Organize samples into groups                               """	drop-down	GeneExpression		Indicates whether AltAnalyze should peform group comparisons or just export interim results and skip filtering steps. Will also use metaprobesets as opposed to agglomerating information from filtered probesets for gene expression calculation.		yes|only export sample data	NA	yes|only export sample data	NA	yes|only export sample data	yes|only export sample data
expression_data_format	"""Expression data format                                         """	"""Expression data format                                         """	"""Expression data format                                               """	"""Expression data format                                        """	drop-down	GeneExpression		Format the user data is in (typically log2 expression values).		log|non-log	log|non-log	log|non-log	log|non-log	log|non-log	log|non-log
normalize_feature_exp	"""Normalize exon/junction expression                   """	"""Normalize exon/junction expression                     """	"""Normalize exon/junction expression                       """	"""Normalize exon/junction expression                      """	drop-down	GeneExpression				NA	NA	NA	NA	NA	RPKM|quantile|none
avg_all_for_ss	"""Determine gene expression levels using               """	"""Determine gene expression levels using                """	"""Determine gene expression levels using                  """	"""Determine gene expression levels using                """	drop-down	GeneExpression		"Indicates whether to average the expression all probesets, as opposed to constitutive only, to calculate a gene expression value for an associated gene."		constitutive probesets|core probesets	NA	constitutive probesets|core probesets	NA	constitutive probesets|known exons	constitutive exons|known exons
include_raw_data	"""Include replicate experiment values in export       """	"""Include replicate experiment values in export       """	"""Include replicate experiment values in export         """	"""Include replicate experiment values in export        """	drop-down	GeneExpression		"Whether or not to include replicate data in the ExpressionBuilder gene expression export file, as opposed to summary statistics (average, t-test p, folds, etc.)."		yes|no	yes|no	yes|no	yes|no	yes|no	yes|no
probability_algorithm	"""Comparison group test statistic                            """	"""Comparison group test statistic                            """	"""Comparison group test statistic                                """	"""Comparison group test statistic                           """	drop-down	GeneExpression				moderated t-test|moderated Welch t-test|unpaired t-test|paired t-test|Kolmogorov Smirnov|Mann Whitney U|Rank Sums	moderated t-test|moderated Welch t-test|unpaired t-test|paired t-test|Kolmogorov Smirnov|Mann Whitney U|Rank Sums	moderated t-test|moderated Welch t-test|unpaired t-test|paired t-test|Kolmogorov Smirnov|Mann Whitney U|Rank Sums	moderated t-test|moderated Welch t-test|unpaired t-test|paired t-test|Kolmogorov Smirnov|Mann Whitney U|Rank Sums	moderated t-test|moderated Welch t-test|unpaired t-test|paired t-test|Kolmogorov Smirnov|Mann Whitney U|Rank Sums	moderated t-test|moderated Welch t-test|unpaired t-test|paired t-test|Kolmogorov Smirnov|Mann Whitney U|Rank Sums
visualize_results	"""Perform expression clustering and visual QC        """	"""Perform expression clustering and visual QC         """	"""Perform expression clustering and visual QC         """	"""Perform expression clustering and visual QC         """	drop-down	GeneExpression				yes|no	yes|no	yes|no	yes|no	yes|no	yes|no
run_lineage_profiler	"""Perform cell profiling with LineageProfiler             """	"""Perform cell profiling with LineageProfiler             """	"""Perform cell profiling with LineageProfiler             """	"""Perform cell profiling with LineageProfiler             """	drop-down	GeneExpression				yes|no	yes|no	yes|no	yes|no	yes|no	yes|no
run_goelite	"""Analyze ontologies and pathways with GO-Elite    """	"""Analyze ontologies and pathways with GO-Elite    """	"""Analyze ontologies and pathways with GO-Elite    """	"""Analyze ontologies and pathways with GO-Elite    """	drop-down	GeneExpression				run immediately|decide later	run immediately|decide later	run immediately|decide later	run immediately|decide later	run immediately|decide later	run immediately|decide later
input_filtered_dir	Select a directory of already filtered AltAnalyze expression files.	Select a directory of already filtered AltAnalyze expression files.	Select a directory of already filtered AltAnalyze expression files.	Select a directory of already filtered AltAnalyze expression files.	folder	InputFilteredFiles	note: all files in this directory should be built by AltAnalyze from a prior analysis.	"note: if not selected, all filtered probe set expression files in\k'AltExpression/<array_type>/<species>'\kwill be used and results written to 'AltResults/AlternativeOutput'.\k"		---	---	---	NA	---	---
input_external_dir	Select a directory with lists of alternative probesets and scores.	Select a directory with lists of alternative probesets and scores.	Select a directory with lists of alternative probesets and scores.	Select a directory with lists of alternative probesets and scores.	folder	InputExternalFiles	"note: all files in this directory should contain probe set IDs and scores\k\k(e.g., FIRMA and MADS results). Files should have at least 3 columns\k(1) probe set ID, (2) normalized fold change and (3) splicing p-value."			---	---	---	NA	---	---
analysis_method	"""Select the alternative exon algorithm                """	"""Select the alternative exon algorithm                 """	"""Select the alternative exon algorithm               """	"""Select the alternative exon algorithm               """	drop-down	AltAnalyze		Alternative exon analysis method to apply to user data.		splicing-index|FIRMA	ASPIRE|linearregres	splicing-index|FIRMA	NA	ASPIRE|linearregres|none	ASPIRE|linearregres|none
additional_algorithms	"""Individual probeset analysis method                 """	"""Individual probeset analysis method                   """	"""Individual probeset analysis method               """	"""Individual probeset analysis method                 """	drop-down	AltAnalyze				NA	NA	NA	NA	splicing-index|FIRMA|none	splicing-index|none
filter_probe_types	"""Select probe sets to include                               """	"""Select probe sets to include                                """	"""Select probe sets to include                               """	"""Select probe sets to include                              """	drop-down	AltAnalyze		Different options for which sets of probe sets to include in the alternative exon analysis.		core|extended|full	all|exons-only|junctions-only|combined-junctions	NA	NA	all|combined-junctions	all|combined-junctions
analyze_all_conditions	"""Type of group comparisons to perform            """	"""Type of group comparisons to perform             """	"""Type of group comparisons to perform          """	"""Type of group comparisons to perform             """	drop-down	AltAnalyze		Different options for which sets of probe sets to include in the alternative exon analysis.		pairwise|all groups|both	pairwise|all groups|both	pairwise|all groups|both	NA	pairwise|all groups|both	pairwise|all groups|both
p_threshold	"""Max MiDAS/normalized intensity p-value       ""  "	"""Max MiDAS/normalized intensity p-value      ""  "	"""Max MiDAS/normalized intensity p-value       ""  "	"""Max MiDAS/normalized intensity p-value     ""  "	enter	AltAnalyze		"Maximum user defined p-value to filter constitutive corrected alternative exon analysis t-test. For AltMouse analyses, only one of the two probe sets is required to meet this threshold."		---	---	---	NA	---	---
alt_exon_fold_cutoff	"""Minimum alternative exon score                       """	"""Minimum alternative exon score                        """	"""Minimum alternative exon score                        """	"""Minimum alternative exon score                      """	enter	AltAnalyze		Fold or ASPIRE minimal score for inclusion with results from the alternative exon analysis (non-log).		---	---	---	NA	---	---
additional_score	"""Individual probeset min alt. exon score            """	"""Individual probeset min alt. exon score             """	"""Individual probeset min alt. exon score             """	"""Individual probeset min alt. exon score             """	enter	AltAnalyze		Fold or ASPIRE minimal score for inclusion with results from the alternative exon analysis (non-log).		NA	---	NA	NA	---	---
permute_p_threshold	"""Maximum reciprocal junction p-value             "" "	"""Maximum reciprocal junction p-value               "" "	"""Maximum reciprocal junction p-value             "" "	"""Maximum reciprocal junction p-value              "" "	enter	AltAnalyze		Maximum allowed permutation p-value.		NA	---	NA	NA	---	---
gene_expression_cutoff	"""Maximum absolute gene-expression change    """	"""Maximum absolute gene-expression change     """	"""Maximum absolute gene-expression change    """	"""Maximum absolute gene-expression change      """	enter	AltAnalyze		Absolute maximum gene-expression fold change allowed between pairwise-comparisons for alternative exon analysis (otherwise gene is excluded).		---	---	---	NA	---	---
remove_intronic_junctions	"""Remove inton-intron novel junctions                   """	"""Remove inton-intron novel junctions                   """	"""Remove inton-intron novel junctions                     """	"""Remove inton-intron novel junctions                   """	drop-down	AltAnalyze		"Indicates whether to remove junctions with splice-site aligning to intron regions only (e.g., I1.1_1234-I1.1_1256)"		NA	NA	NA	NA	NA	yes|no
perform_permutation_analysis	"""Perform permutation analysis                               """	"""Perform permutation analysis                               """	"""Perform permutation analysis                                   """	"""Perform permutation analysis                              """	drop-down	AltAnalyze		Indicates whether to perform permutation analysis of ASPIRE or linearegress scores to calculate a statistical likelihood value.		NA	yes|no	NA	NA	yes|no	yes|no
export_splice_index_values	"""Export all normalized intensities                                                                  """	"""Export all normalized intensities                                                                    """	"""Export all normalized intensities                                                                   """	"""Export all normalized intensities                                                                    """	single-checkbox	AltAnalyze		Export raw constitutive corrected probe set expression values for replicates. Useful for expression clustering of alternative exon changes.		yes|no	yes|no	yes|no	NA	yes|no	yes|no
run_MiDAS	"""Calculate MiDAS p-values                                                                            """	"""Calculate MiDAS p-values                                                                            """	"""Calculate MiDAS p-values                                                                             """	"""Calculate MiDAS p-values                                                                            """	single-checkbox	AltAnalyze		Export re-formatted input for analysis in MiDAS through an external application (Affymetrix Power Tools).		yes|no	NA	yes|no	NA	yes|no	yes|no
calculate_splicing_index_p	"""Calculate normalized intensity p-values                                                      """	"""Calculate normalized intensity p-values                                                        """	"""Calculate normalized intensity p-values                                                      """	"""Calculate normalized intensity p-values                                                        """	single-checkbox	AltAnalyze				yes|no	NA	yes|no	NA	NA	NA
filter_for_AS	"""Filter results for predicted AS                                                                       """	"""Filter results for predicted AS                                                                        """	"""Filter results for predicted AS                                                                        """	"""Filter results for predicted AS                                                                       """	single-checkbox	AltAnalyze				yes|no	yes|no	yes|no	NA	yes|no	yes|no
analyze_functional_attributes	"""Align probesets to protein domains using            """	"""Align probesets to protein domains using             """	"""Align probesets to protein domains using              """	"""Align probesets to protein domains using              """	drop-down	AltAnalyze				direct-alignment|inferred comparison	direct-alignment|inferred comparison	direct-alignment|inferred comparison	NA	direct-alignment|inferred comparison	direct-alignment|inferred comparison
microRNA_prediction_method	"""Number of algorithms required for miRNA            \kbinding site reporting                                           """	"""Number of algorithms required for miRNA          \kbinding site reporting                                          """	"""Number of algorithms required for miRNA          \kbinding site reporting                                              """	"""Number of algorithms required for miRNA          \kbinding site reporting                                        """	drop-down	AltAnalyze		Include binding sites only present in multiple analyzed micoRNA target databases or in at least one databases.		one|two or more	one|two or more	one|two or more	NA	one|two or more	one|two or more
pick_filtering_options	Filter results by which algorithms	Filter results by which algorithms	Filter results by which algorithms	Filter results by which algorithms	multiple-checkbox	Advanced				SI fold|SI p-value|MiDAS p-value	NA	NA	NA	NA	NA
avg_all_for_ss_for_AS	Use known exons probesets\k to derive gene expression\k versus constitutive only	Use known exons probesets\k to derive gene expression\k versus constitutive only	Use known exons probesets\k to derive gene expression\k versus constitutive only	Use known exons probesets\k to derive gene expression\k versus constitutive only	radio	Advanced				constitutive probesets|known exons	constitutive probesets|known exons	NA	NA	constitutive probesets|known exons	constitutive exons|known exons
new_species_code	Two letter species code (e.g. Hs)     	Two letter species code (e.g. Hs)     	Two letter species code (e.g. Hs)     	Two letter species code (e.g. Hs)     	enter	NewSpecies				---	---	---	---	---	---
new_species_name	Species name (e.g. Homo sapiens)  	Species name (e.g. Homo sapiens)  	Species name (e.g. Homo sapiens)  	Species name (e.g. Homo sapiens)  	enter	NewSpecies				---	---	---	---	---	---
new_manufacturer	Choose vendor	Choose vendor	Choose vendor	Choose vendor	drop-down	NewSpecies				---	---	---	---	---	---
allowed_array_systems	Choose array or data-type	Choose array or data-type	Choose array or data-type	Choose array or data-type	drop-down	NewSpecies2				---	---	---	---	---	---
ge_fold_cutoffs	"""Minimum gene expression fold change              """	"""Minimum gene expression fold change              """	"""Minimum gene expression fold change              """	"""Minimum gene expression fold change              """	enter	GOElite				---	---	---	---	---	---
ge_pvalue_cutoffs	"""Maximum gene expression ttest p-value           """	"""Maximum gene expression ttest p-value           """	"""Maximum gene expression ttest p-value             """	"""Maximum gene expression ttest p-value           """	enter	GOElite				---	---	---	---	---	---
ge_ptype	"""Filter based on the following p-value                """	"""Filter on this type of gene expression p-value        """	"""Filter on this type of gene expression p-value          """	"""Filter on this type of gene expression p-value        """	drop-down	GOElite				rawp|adjp	rawp|adjp	rawp|adjp	rawp|adjp	rawp|adjp	rawp|adjp
filter_method	"""Prune Ontology terms using                              """	"""Prune Input GO terms and Pathways ranking by:    """	"""Prune Input GO terms and Pathways ranking by:    """	"""Prune Input GO terms and Pathways ranking by:    """	drop-down	GOElite				z-score|gene number|combination	z-score|gene number|combination	z-score|gene number|combination	z-score|gene number|combination	z-score|gene number|combination	z-score|gene number|combination
z_threshold	"""Z-score cutoff for initial filtering (> 0)               """	"""Enter a  Z-score cutoff for initial filtering (> 0)     """	"""Enter a  Z-score cutoff for initial filtering (> 0)    """	"""Enter a  Z-score cutoff for initial filtering (> 0)     """	enter	GOElite				---	---	---	---	---	---
p_val_threshold	"""Enter permuted p-value cutoff (between 0-1)    """	"""Enter permuted p-value cutoff (between 0-1)    """	"""Enter permuted p-value cutoff (between 0-1)     """	"""Enter permuted p-value cutoff (between 0-1)    """	enter	GOElite				---	---	---	---	---	---
change_threshold	"""Enter minimum number of changed genes         """	"""Enter minimum number of changed genes         """	"""Enter minimum number of changed genes         """	"""Enter minimum number of changed genes         """	enter	GOElite				---	---	---	---	---	---
ORA_algorithm	"""Select the algorithm to use for ORA                   """	"""Select the algorithm to use for ORA                   """	"""Select the algorithm to use for ORA                       """	"""Select the algorithm to use for ORA                   """	drop-down	GOElite				Permute p-value|Fisher Exact Test	Permute p-value|Fisher Exact Test	Permute p-value|Fisher Exact Test	Permute p-value|Fisher Exact Test	Permute p-value|Fisher Exact Test	Permute p-value|Fisher Exact Test
resources_to_analyze	"""Only analyze the following resource(s)               """	"""Analyze Pathways or Gene Ontology                       """	"""Analyze Pathways or Gene Ontology                     """	"""Analyze Pathways or Gene Ontology                       """	drop-down	GOElite				all|Pathways|Gene Ontology	all|Pathways|Gene Ontology	all|Pathways|Gene Ontology	all|Pathways|Gene Ontology	all|Pathways|Gene Ontology	all|Pathways|Gene Ontology
pathway_permutations	"""Number of permutations for ORA                       """	"""Number of permutations for ORA                       """	"""Number of permutations for ORA                         """	"""Number of permutations for ORA                       """	enter	GOElite				---	---	---	---	---	---
mod	"""Select primary relational gene system                """	"""Select the primary relational gene database used   """	"""Select the primary relational gene database used"""	"""Select the primary relational gene database used   """	drop-down	GOElite				Ensembl	EntrezGene	Ensembl	Ensembl|EntrezGene	Ensembl	Ensembl
get_additional	"""Download/update additional resources              """	"""Download/update additional resources              """	"""Download/update additional resources                """	"""Download/update additional resources              """	drop-down	GOElite				None	None	None	None	None	None
elite_input_dir	Select a directory of GO-Elite formatted input file(s).	Select a directory of GO-Elite formatted input file(s).	Select a directory of GO-Elite formatted input file(s).	Select a directory of GO-Elite formatted input file(s).	folder	InputGOEliteFiles				---	---	---	---	---	---
elite_denom_dir	Select a directory of GO-Elite formatted denominator file(s).	Select a directory of GO-Elite formatted denominator file(s).	Select a directory of GO-Elite formatted denominator file(s).	Select a directory of GO-Elite formatted denominator file(s).	folder	InputGOEliteFiles				---	---	---	---	---	---
elite_output_dir	Select an GO-Elite output directory	Select an GO-Elite output directory	Select an GO-Elite output directory	Select an GO-Elite output directory	folder	InputGOEliteFiles	"note: by default, the output will be stored in a set of new directories under\kthe same directory as the input expression file."			---	---	---	---	---	---
input_cluster_file	Select the tab-delimited expression file for clustering	Select the tab-delimited expression file	Select the tab-delimited expression file	Select the tab-delimited expression file	file	heatmap	note: the expression file must have an annotation row and annotation column.\k Log2 values recommended. Results saved to the folder 'DataPlots'.\k			---	---	---	---	---	---
column_metric	Select the column clustering metric	Select the column clustering metric	Select the column clustering metric	Select the column clustering metric	comboBox	heatmap		http://docs.scipy.org/doc/scipy/reference/spatial.distance.html	euclidean	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule
column_method	Select the column clustering method	Select the column clustering method	Select the column clustering method	Select the column clustering method	comboBox	heatmap		http://docs.scipy.org/doc/scipy/reference/cluster.hierarchy.html	single	average|single|complete|weighted	average|single|complete|weighted	average|single|complete|weighted	average|single|complete|weighted	average|single|complete|weighted	average|single|complete|weighted
row_metric	Select the row clustering metric	Select the row clustering metric	Select the row clustering metric	Select the row clustering metric	comboBox	heatmap		http://docs.scipy.org/doc/scipy/reference/spatial.distance.html	cosine	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule	braycurtis|canberra|chebyshev|cityblock|correlation|cosine|dice|euclidean|hamming|jaccard|kulsinski|mahalanobis|matching|minkowski|rogerstanimoto|russellrao|seuclidean|sokalmichener|sokalsneath|sqeuclidean|yule
row_method	Select the row clustering method	Select the row clustering method	Select the row clustering method	Select the row clustering method	comboBox	heatmap		http://docs.scipy.org/doc/scipy/reference/cluster.hierarchy.html	average	average|single|complete|weighted	average|single|complete|weighted	average|single|complete|weighted	average|single|complete|weighted	average|single|complete|weighted	average|single|complete|weighted
color_selection	Choose a color scheme	Choose a color scheme	Choose a color scheme	Choose a color scheme	comboBox	heatmap	note: colors are indicated as up-null-down	http://matplotlib.sourceforge.net/examples/pylab_examples/show_colormaps.html	red-white-blue	red-white-blue|red-black-sky|red-black-blue|red-black-green|yellow-black-blue|green-white-purple|coolwarm|seismic	red-white-blue|red-black-sky|red-black-blue|red-black-green|yellow-black-blue|green-white-purple|coolwarm|seismic	red-white-blue|red-black-sky|red-black-blue|red-black-green|yellow-black-blue|green-white-purple|coolwarm|seismic	red-white-blue|red-black-sky|red-black-blue|red-black-green|yellow-black-blue|green-white-purple|coolwarm|seismic	red-white-blue|red-black-sky|red-black-blue|red-black-green|yellow-black-blue|green-white-purple|coolwarm|seismic	red-white-blue|red-black-sky|red-black-blue|red-black-green|yellow-black-blue|green-white-purple|coolwarm|seismic
cluster_rows	Cluster rows	Cluster rows	Cluster rows	Cluster rows	comboBox	heatmap			yes	yes|no	yes|no	yes|no	yes|no	yes|no	yes|no
cluster_columns	Cluster columns	Cluster columns	Cluster columns	Cluster columns	comboBox	heatmap			yes	yes|no	yes|no	yes|no	yes|no	yes|no	yes|no
transpose	Transpose matrix	Transpose matrix	Transpose matrix	Transpose matrix	comboBox	heatmap			no	yes|no	yes|no	yes|no	yes|no	yes|no	yes|no
input_cluster_file	Select the tab-delimited expression file for clustering	Select the tab-delimited expression file	Select the tab-delimited expression file	Select the tab-delimited expression file	file	PCA	note: the expression file must have an annotation row and annotation column.\k Log2 values recommended. Results saved to the folder 'DataPlots'.\k			---	---	---	---	---	---
transpose	Transpose matrix	Transpose matrix	Transpose matrix	Transpose matrix	comboBox	PCA			no	yes|no	yes|no	yes|no	yes|no	yes|no	yes|no
input_lineage_file	Select the tab-delimited expression file for LineageProfiler	Select the tab-delimited expression file for LineageProfiler	Select the tab-delimited expression file for LineageProfiler	Select the tab-delimited expression file for LineageProfiler	file	LineageProfiler	note: This function visualizes samples rather than groups. To visualize groups\krun LineageProfiler using the 'Process Expression File' main menu option.\k\k The expression file must have an annotation row and annotation column.\k Log2 values recommended. Results saved to the folder 'DataPlots'.\k			---	---	---	---	---	---
