Man pages for njmadrid/RNAseqQuality
Provides a set of functions for summarizing the quality of RNA-seq data.
| BinCounts | Get mean read coverage from 5’ to 3’ across the most highly... |
| CreateSpliceJunctionTable | Create a table of unique splice junction expression per tab... |
| GetAlignmentStatistics | Get a summary of alignment statistics for an aligned bam file... |
| GetBedGraphRefSeqOverlaps | Get overlaps using GenomicRanges findOverlaps for a bedgraph... |
| GetCountsPerRegion | Count the number of reads that are in a given genomic region. |
| GetCoverageMatrix | Get coverage matrix for genes which are highly expressed in... |
| GetHtseqSummaryStats | Read and organize htseq *_summary_stats.txt files into one... |
| GetNumGenesExpressed | Get the total number of genes expressed per gtf file... |
| GetPileUpPerGene | Get read depths per gene as defined by the RSamtools pileup... |
| GetrRNAStatistics | Get the total number of rRNA read counts from bam file.... |
| GetTranscriptomeCoverage | Calculate a coverage score based on read depth and also gene... |
| OverlapEditSites | Overlap bedgraph coverage file (*.bedgraph.gz) with known... |
| SummarizeUniqueReads | Get a summary of the unique reads from bam file. Duplicate... |
