API for andrewtikhonov/ArrayExpressHTS
ArrayExpress High Throughput Sequencing Processing Pipeline
| Global functions | |
|---|---|
| .onLoad | Source code |
| .onUnload | Source code |
| ASCIIconvert | Source code |
| ArrayExpressHTS | Man page Source code |
| ArrayExpressHTSFastQ | Man page Source code |
| addOptions | Source code Source code |
| addPackageVariables | Source code Source code |
| addPathToPATH | Source code |
| align | Source code |
| align_bowtie | Source code |
| align_bwa | Source code |
| align_tophat | Source code |
| annot_to_iranges | Source code |
| appendStatusText | Source code |
| assignOneProject | Source code |
| assignPipelineOptions | Source code Source code |
| assignProjects | Source code |
| assignStopOnWarnings | Source code |
| assignSubmID | Source code |
| attachExperimentData | Source code |
| bamParam | Source code |
| bam_to_list | Source code |
| bam_to_occurrencetab | Source code |
| bamlist_to_alignedread | Source code |
| calculate_dustyScore | Source code |
| call_count | Source code |
| call_cufflinks | Source code |
| call_estimator | Source code |
| call_mmseq | Source code |
| call_none | Source code |
| call_normalisator | Source code |
| call_samtools | Source code |
| call_tmm | Source code |
| checkAndDefineBasePath | Source code Source code |
| checkAndDefineReferencePath | Source code Source code |
| checkAndDefineToolOptions | Source code Source code |
| checkOneTool | Source code Source code |
| checkProjectErrors | Source code |
| checkReference | Source code |
| checkToolExists | Source code Source code |
| checkURLAvailable | Source code |
| checkURLResourcesAvailable | Source code |
| check_indexes | Source code |
| cleanupAfterExecution | Source code |
| cleanupCluster | Source code |
| compareProjects | Source code |
| count_polyL | Source code |
| count_reads_per_feature | Source code |
| createAEprojects | Source code |
| createDefaultProject | Source code |
| createDirAndBackup | Source code |
| createFastQProjects | Source code |
| createOptions | Source code Source code |
| createServerLog | Source code |
| create_feature_data | Source code |
| cufflinks_to_countmatrix | Source code |
| cufflinks_to_dataframe | Source code |
| cufflinks_to_granges | Source code |
| cufflinks_to_iranges | Source code |
| downloadENADataFile | Source code |
| download_annotation | Source code |
| exprs_table_to_dataframe | Source code |
| fasta_to_list | Source code |
| fastq_to_dataframe | Source code |
| fastq_to_shortreadq | Source code |
| fastqquality_to_integer | Source code |
| filterENAData | Source code |
| filter_chr | Source code |
| filter_shortread_by_sequence | Source code |
| filterbam | Source code |
| finalCountdown | Source code |
| findUsefulRange | Source code |
| fixReference | Source code |
| fixReferenceDoubleY | Source code |
| fixedOptions | Source code |
| flagToBitStr | Source code |
| flag_is_firstmate | Source code |
| flag_is_mapped | Source code |
| flag_is_mapped_and_proper | Source code |
| flag_is_secondmate | Source code |
| flag_meaning | Source code |
| flagint_to_bit | Source code |
| getAEExpDescription | Source code |
| getAEExpType | Source code |
| getAEExperimentPathBase | Source code |
| getAEIDFFilename | Source code |
| getAEIDFURL | Source code |
| getAERawDataFilenames | Source code |
| getAESDRFFilename | Source code |
| getAESDRFURL | Source code |
| getAlignerDefaultOptions | Source code |
| getAllHTSAccessionsFromAE | Source code |
| getAssayNameFromSDRF | Source code |
| getCluster | Source code |
| getCurrentRefVersion | Source code |
| getDataFromSDRF | Source code |
| getDefaultFilteringOptions | Man page Source code |
| getDefaultProcessingOptions | Man page Source code |
| getDefaultRCloudOptions | Man page Source code |
| getDefaultReferenceDir | Source code |
| getENAAccessionPrefixes | Source code |
| getENAAccessionRecord | Source code |
| getENAExpIDForAEAcc | Source code |
| getENAExpIDFromSDRF | Source code |
| getENAFastqPathBase | Source code |
| getENAFastqURLBase | Source code |
| getENARunIDForExpID | Source code |
| getEnsemblAnnotation | Source code |
| getEnsemblReference | Source code |
| getExpStatus | Source code |
| getExperimentDescriptors | Source code |
| getFactorValueFromSDRF | Source code |
| getFirstAvailableLayout | Source code |
| getHTSAccessionsFromAE | Source code |
| getHTSRNASeqAccessionsFromAE | Source code |
| getLibrarySelectionFromSDRF | Source code |
| getLibraryStrategyFromSDRF | Source code |
| getMark | Source code |
| getMatchedText | Source code |
| getOptionPathComponent | Source code |
| getOrganismFromSDRF | Source code |
| getPackageVariable | Source code Source code |
| getPipelineOption | Man page Source code Source code |
| getPipelineOptions | Man page Source code Source code |
| getReadLength0 | Source code |
| getRunIDFromSDRF | Source code |
| getRunStatus | Source code |
| getSAMLineInfo | Source code |
| getSDRFforAccession | Source code |
| getSubmID | Source code |
| getSupportedOrganisms | Source code |
| getSupportedSelectionRowIndexes | Source code |
| getSupportedStrategyRowIndexes | Source code |
| getToolName | Source code Source code |
| getToolOptionNames | Source code Source code |
| getTraceMark | Source code Source code |
| get_DE | Source code |
| get_annotation | Source code |
| get_annotation_RData_name | Source code |
| get_chr_representation | Source code |
| get_fastq_quality0 | Source code |
| get_fastq_quality_scale | Source code |
| grepAllENAAccessions | Source code |
| grepSDRFForENAAccessions | Source code |
| gtf_to_dataframe | Source code |
| indexReference | Source code |
| initDefaultProject | Source code |
| initEnvironmentVariables | Source code |
| initPackageVariables | Source code Source code |
| initPipelineOptions | Source code Source code |
| isOrganismSupported | Source code |
| isPackageVariableDefined | Source code Source code |
| isRCloud | Man page Source code |
| is_polyX | Source code |
| length_raw_reads | Source code |
| loadENAData | Source code |
| locateInSystem | Source code Source code |
| locateInToolBase | Source code Source code |
| log.error | Source code |
| log.info | Source code |
| log.warning | Source code |
| makeAEFilesURL | Source code |
| makeAEIDFURL | Source code |
| makeAESDRFFilenames | Source code |
| makeAESDRFURLs | Source code |
| makeClusterLogFolder | Source code |
| makeENAExpURL | Source code |
| makeENAFastqFileName | Source code |
| makeENAFastqURL | Source code |
| make_filt_indexes | Source code |
| make_indexes_old | Source code |
| mapAEtoENAviaENADataFile | Source code |
| mapAEtoENAviaHTTP | Source code |
| map_quality_scale0 | Source code |
| mergeOptions | Source code |
| mmseq_to_dataframe | Source code |
| move_files | Source code |
| number_aligned_reads | Source code |
| number_raw_reads | Source code |
| obtainENAFastQDataFiles | Source code |
| parseFlag | Source code |
| peekPSRExpId | Source code |
| peekPSRFolder | Source code |
| peekPSRRunId | Source code |
| phred_to_average_qual | Source code |
| phred_to_avgqual | Source code |
| pileup_to_dataframe | Source code |
| plot_DE_length | Source code |
| plot_DE_report | Source code |
| plot_N_distrib | Source code |
| plot_aligned_report | Source code |
| plot_avgbasequal_boxplots | Source code |
| plot_avgbasequal_distrib | Source code |
| plot_bars_totalunique | Source code |
| plot_basecall_per_cycle | Source code |
| plot_basecall_per_cycle_log | Source code |
| plot_chromosome_distrib | Source code |
| plot_compared_hits | Source code |
| plot_compared_raw_report | Source code |
| plot_dustyScore_distrib | Source code |
| plot_dustyScore_distribs | Source code |
| plot_hits | Source code |
| plot_insertsize | Source code |
| plot_insize_boxplot | Source code |
| plot_mapq | Source code |
| plot_mapq_distribution | Source code |
| plot_multiplealigns_hist | Source code |
| plot_multiplealigns_vs_complexity | Source code |
| plot_polyX | Source code |
| plot_quality_per_cycle | Source code |
| plot_ranges | Source code |
| plot_raw_report | Source code |
| plot_readoccurence_cdf | Source code |
| plot_repeatedreads_vs_complexity | Source code |
| plot_scatter_samples | Source code |
| plot_strand_distrib | Source code |
| plot_transcript_distrib | Source code |
| pokePSRExpId | Source code |
| pokePSRFolder | Source code |
| pokePSRRunId | Source code |
| polyX_size | Source code |
| prepareAnnotation | Man page Source code |
| prepareCluster | Source code |
| prepareReference | Man page Source code |
| print.memory.usage | Source code |
| printFlag | Source code |
| processOneProject | Source code |
| processOneProjectAlignment | Source code |
| processOneProjectAlnReport | Source code |
| processOneProjectEstimation | Source code |
| processOneProjectRawReport | Source code |
| projectSummary | Source code |
| readData | Source code |
| readENADataForExpID | Source code |
| readENADataForRunID | Source code |
| readIDF | Source code |
| readSDRF | Source code |
| read_gtf | Source code |
| recordAlignedProperties | Source code |
| reflen_to_dataframe | Source code |
| reftype_to_filename | Source code |
| registerExpStepCompleted | Source code |
| registerExpStepFailure | Source code |
| registerExpStepStarted | Source code |
| registerExpStepStatusText | Source code |
| registerExpStepWarning | Source code |
| registerRunStepCompleted | Source code |
| registerRunStepFailure | Source code |
| registerRunStepStarted | Source code |
| registerRunStepStatusText | Source code |
| registerRunStepWarning | Source code |
| removePathFromPATH | Source code |
| replacePathInPATH | Source code |
| resetProjectErrors | Source code |
| runProjects | Source code |
| run_cmds | Source code |
| sam_addXS | Source code |
| scanAllENAData | Source code |
| scanSupportedOrganisms | Source code |
| searchBiomart | Source code |
| sendReminder | Source code |
| setCluster | Source code |
| setExpStatus | Source code |
| setPackageVariable | Source code Source code |
| setPipelineOption | Source code Source code |
| setPipelineOptions | Man page Source code Source code |
| setProjectData | Source code |
| setRunStatus | Source code |
| setUserOptions | Source code |
| setupBaseFolder | Source code |
| setupDataFolder | Source code |
| setupPSRFolder | Source code |
| setupPSRLogging | Source code |
| setupSUBM_ID | Source code |
| shortread_to_dataframe | Source code |
| shortread_to_tab | Source code |
| shortread_to_unique | Source code |
| standardise | Source code |
| std | Source code |
| stringids_to_dataframe | Source code |
| stringset_to_dustyscore | Source code |
| stripOffQuotas | Source code |
| table_pileup_summary | Source code |
| table_transcript_overlap | Source code |
| table_transcriptome_vs_genome | Source code |
| to_dataframe | Source code |
| to_expressionset | Source code |
| toolFolderName | Source code Source code |
| trace.enter | Source code Source code |
| trace.exit | Source code Source code |
| transcriptome_to_dataframe | Source code |
| un_std | Source code |
| updateExpStatusOnExit | Source code |
| updateRunStatusOnExit | Source code |
| verify_fqfiles | Source code |
| writePropertyFile | Source code |
| xstringset_to_hitcount | Source code |
