# TSSr: A package for transcription start site sequencing data analyses.

`TSSr-class.Rd`

TSSr is designed to analyze transcription start sites (TSSs) and core promoters with most types of 5’end sequencing data, such as cap analysis of gene expression (CAGE) (Takahashi, Lassmann et al. 2012), no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) (Murata, Nishiyori-Sueki et al. 2014), a Super-Low Input Carrier-CAGE (SLIC-CAGE) (Cvetesic, Leitch et al. 2018), NanoCAGE (Cumbie, Ivanchenko et al. 2015), TSS-seq (Malabat, Feuerbach et al. 2015), transcript isoform sequencing (TIF-seq) (Pelechano, Wei et al. 2013), transcript-leaders sequencing (TL-seq) (Arribere and Gilbert 2013), precision nuclear run-on sequencing (PRO-Cap) (Mahat, Kwak et al. 2016), and GRO-Cap/5’GRO-seq (Kruesi, Core et al. 2013).

## Details

TSSr package provides a comprehensive workflow on TSS data starts from identification of accurate TSS locations, clustering TSSs within small genomic regions corresponding to core promoters, and transcriptional activity quantifications, as well as specialized downstream analyses including core promoter shape, cluster annotation, gene differential expression, core promoter shift. TSSr can take multiple formats of files as input, such as Binary Sequence Alignment Mao (BAM) files (single-ended or paired-ended), Browser Extension Data (bed) files, BigWig files, ctss files or tss tables. TSSr also generates various types of TSS or core promoter track files which can be visualized in the UCSC Genome Browser or Integrative Genomics Viewer (IGV). TSSr also exports downstream analyses result tables and plots. Multiple cores are supported on Linux or Mac platforms.

## Slots

`genomeName`

  character.

`inputFiles`

  character.

`inputFilesType`

  character.

`sampleLabels`

  character.

`sampleLabelsMerged`

  character.

`librarySizes`

  numeric.

`TSSrawMatrix`

  data.frame.

`mergeIndex`

  numeric.

`TSSprocessedMatrix`

  data.frame.

`tagClusters`

  list.

`consensusClusters`

  list.

`clusterShape`

  list.

`refSource`

  character.

`organismName`

  character.

`assignedClusters`

  list.

`unassignedClusters`

  list.

`filteredClusters`

  list.

`DEtables`

  list.

`PromoterShift`

  list.