|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...|
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