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 |
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