A NGS analysis pipeline.
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Documentation for package ‘HTSeqGenie’ version 4.30.0
Help Pages
| analyzeVariants | Calculate and process Variants |
| annotateVariants | Annotate variants via vep |
| buildGenomicFeaturesFromTxDb | Build genomic features from a TxDb object |
| callVariantsGATK | Variant calling via GATK |
| checkGATKJar | Check for the GATK jar file |
| detectRRNA | Detect rRNA Contamination in Reads |
| excludeVariantsByRegions | Filter variants by regions |
| gatk | gatk |
| generateSingleGeneDERs | generateSingleGeneDERs |
| getRRNAIds | Detect reads that look like rRNA |
| getTabDataFromFile | Load tabular data from the NGS pipeline result directory |
| hashCoverage | Hashing function for coverage |
| hashVariants | Hashing function for variants |
| hashVector | Hashing function for vector |
| HTSeqGenie | Package overview |
| isSparse | isSparse |
| markDuplicates | markDuplicates |
| markDups | markDups |
| realignIndels | realignIndels |
| realignIndelsGATK | Realign indels via GATK |
| runPipeline | Run the NGS analysis pipeline |
| runPipelineConfig | Run the NGS analysis pipeline |
| setupTestFramework | setup test framework |
| TP53GenomicFeatures | Demo genomic features around the TP53 gene |
| vcfStat | Compute stats on a VCF file |
| wrap.callVariants | Variant calling |
| writeVCF | writeVCF |