Man pages for carmencita/CHIC
Quality Control Pipeline for ChIP-Seq Data
| chicWrapper | ChIC analysis in one command |
| createMetageneProfile | Wrapper function to create scaled and non-scaled... |
| downsample_ChIPpeaks | Function for downsampling peaks in ChIP-data to simulate... |
| getCrossCorrelationScores | QC-metrics from cross-correlation profile, phantom peak and... |
| getPeakCallingScores | Calculating QC-values from peak calling procedure |
| listAvailableElements | Shows available chromatin marks and factors |
| listDatasets | Lists the IDs of samples included in the compendium |
| listMetrics | Lists the metrics available in the compendium |
| metagenePlotsForComparison | Function to create metage plots for comparison |
| plotReferenceDistribution | Function to create reference distribution plot for comparison |
| predictionScore | Predict score |
| qualityScores_EM | Wrapper function to calculate EM metrics |
| qualityScores_GM | Wrapper function to calculate GM metrics from global read... |
| qualityScores_LM | Wrapper function that plots non-scaled profiles for TSS of... |
| qualityScores_LMgenebody | Wrapper function to plot the scaled metagene- profile and to... |
| readBamFile | Read bam file |
| removeLocalTagAnomalies | Removes loval anomalies |
| tagDensity | Smoothed tag density |
