Man pages for Linlab-slu/TSSr
TSS sequencing data analysis
| annotateCluster | Annotate clusters with GFF annotation file. |
| callEnhancer | Identification of enhancers |
| clusterTSS | Cluster TSSs into tag clusters |
| consensusCluster | Make consensus clusters across multiple samples. |
| deGene | Analysis of gene differential expression. |
| exampleTSSr | TSSr example data |
| exportClustersTable | Export cluster tables |
| exportClustersToBed | Creating bed files of clusters |
| exportDETable | Export gene differential expression results table |
| exportEnhancerTable | Export enhancer tables |
| exportShapeTable | Export core promoter shape score tables |
| exportShiftTable | Export core promoter shift table |
| exportTSStable | Export TSS tables |
| exportTSStoBedgraph | Creating Bedgraph/BigWig tracks of TSSs |
| filterTSS | Filter raw TSS counts or normalized TSS |
| getTSS | Precisely identify TSSs from bam files, paired end bam files,... |
| mergeSamples | Merge TSS samples |
| normalizeTSS | Normalize raw TSS counts |
| plotCorrelation | Pairwise scatter plots and correlations of TSS signal |
| plotDE | Plot gene differential expressions |
| plotInterQuantile | Plot core promoter interquantile width |
| plotShape | Plot core promoter shape |
| plotTSS | Plot TSSs and clusters |
| plotTssPCA | Plotting principle component analysis (PCA) |
| shapeCluster | Analysis of core promoter shape |
| shiftPromoter | Select genes which have core promoter shift across different... |
| TSSr-class | TSSr: A package for transcription start site sequencing data... |
| TSSr-package | TSSr: A package for transcription start site sequencing data... |
