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Table 2 Examples of software packages for analyzing 5′-end data (including CAGE)

From: CAGEfightR: analysis of 5′-end data using R/Bioconductor

Tool Implementation Input data Tag Clustering TSS candidate shape Differential Expression Gene-level analysis Unique features
MOIRAI [29] Graphical User Interface FASTQ paraclu [30] None None inbuilt None rRNAdust, TagDust [31]
RECLU [32] Bash BED modified paraclu [30] None edgeR [33] None Hierarchical TSSs
CAGEr [34] R/Bioconductor BAM distance or paraclu [30] IQR DESeq2 [35] Gene expression G-bias correction [36], power-law normalization, TSS shifts
icetea [37] R/Bioconductor FASTQ Sliding window None edgeR [33] Gene expression Paired-end methods, mapping via R
TSRchitect [38] R/Bioconductor BAM X-means Shape Index [17] None inbuilt None Paired-end methods
CAGEfightR R/Bioconductor BigWig Slice-reduce IQR, entropy, etc. None inbuilt Gene expression and alternative TSS usage Enhancer calling, TSS-enhancer co-expression, super enhancers