Man pages for nixstix/RNASeqAnalysis
Analysis of RNA-Seq data: QC filtering, expression analysis, differential expression pipeline
| addKallistoResToTable | Adds the output kallisto directory to the original datafile. |
| availableReferences | A number of transcriptome indices have already been built,... |
| checkDataFile | Checks that the format of the "data file" (which is used as... |
| collectKallistoCounts | Collects raw counts of gene (or transcript) data generated by... |
| collectKallistoCountsTXItoGene | Collects raw counts of genes, based on transcript data... |
| compareQA | Compares quality before and after filtering fastq files.... |
| datafileTemplate | (Empty) template data file which summarises the data to be... |
| filterBadSeqs | Performs quality checks, then filters reads for quality |
| kallistoIndex | Builds a transcriptome index (.idx) from a FASTA-formatted... |
| kallistoQuant | Kallisto quantifies transcript abundance from RNA-Seq data. |
| runQA | Performs quality checks |
| summariseFilteringStats | Collects summary statistics on filtering This function... |
