Man pages for RGLab/RNASeqPipelineR
Construct Standardized pipelines for processing RNASeq data
| AlignmentSTAR | Use the STAR tool to align the reads |
| annotateSRA | Annotate the SRA file pData |
| annotateUCSC | Annotate features: map UCSC gene cluster id to gene symbols |
| annotationsFromSRX | Quick and dirty annotations from SRAmetadb |
| assignConfig | Assign a new element to the RNASeqPipelineR configuration |
| buildGenomeIndexSTAR | Build a genome index for STAR |
| buildGenomeIndexSTAR2 | Build a reference genome 2 |
| buildReference | Build a reference genome |
| concatenateFastq | Concatenate FastQ files |
| configure_project | Configure the project and store info in namespace |
| convertSRAtoFastQ | Convert SRA files to FastQ |
| createProject | Create a new RNASeqPipeline project |
| detectAspera | Detect and configure the aspera client location |
| devel_truncateData | Utility function to truncate the test data to 'n' SRA files... |
| downloadSRA | Download FastQ files based on Immport data and SRA db, unless... |
| getAndConnectSRAdb | Checks if the SRAdb sqlite database is available |
| getConfig | Get the configuration for the project from the namespace |
| getConfigDir | Retrieve full path to 'dir' in project configuration... |
| getConfigFile | Retrieve full path to 'dir/file' in project configuration... |
| getDataFromSRX | Download SRA files from SRX accessions |
| getDir | Obtain directory path for configuration variable. |
| getExpressionSet | Return and expression set of the counts or TPM values |
| kallistoAlign | Use the Kallisto tool to align and quantify RNASeq FASTQ... |
| kallistoAssembleOutput | Assemble kallisto output into a single table. |
| kallistoAssembleQC | Collect kallisto and fastqc information. |
| kallistoBuildTranscriptIndex | kallisto methods |
| kallistoReadQC | Assemble kallisto quality control information |
| loadImmportTables | Load data from Immport tables |
| loadProject | Load an RNASeqPipelineR project |
| mergeData | Map the annotation file to the count and tpm data |
| MiTCR | Run MiTCR on each fastQ file |
| pear | Run PEAR to assemble paired-end fastq files into one files. |
| pipelineReport | Produce a report listing the tools and packages used by the... |
| QualityControl | Generate QualityControl Matric. |
| qualityRNASeQC | Run RNASeQC quality control |
| readConfig | Read the configuration for a project |
| RNASeqPipeline | Simplify pipelining RNASeq data |
| RSEMAssembleExpressionMatrix | Assemble an expression matrix of all results |
| RSEMCalculateExpression | Use the RSEM tool to annotate and quantify the reads |
| RSEMSummarizeMapping | Summarize the number of mapped, unmapped and ambiguous reads... |
| runFastQC | Perform FastQC quality control |
| saveConfig | Save the configuration for a project |
| sequenceAlignmentTopHat | Use the Tophat tool to align reads |
| setGenomeReference | Set path to reference genome index |
| SRAOverview | Overview of downloaded files |
| sumDuplicates | Sum all read counts for multiple instances of a single gene... |
| summarizeDuplication | Summarize duplication statistics from fastqc |
| summarizeFastQC | Summarize the fastQC results |
