Intends to detect clusters from data attached to sequence. Paraclu identifies clusters in genomic data and uses a density parameter for reporting the segments of each chromosome. It allows users to describe the structure of data.
Creates transcript assemblies from CAGEScan derived Transcription Start Site (TSS) associated reads paired with randomly primed readsm, grouping them on the basis of the common location of TSS reads. Assembly-seeding TSS read clusters can either be provided as an external BED file or computed from the CAGEscan data itself.
Provides a comprehensive toolbox for analysis and visualization of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites (TSS) and promoterome mining in R. CAGEr performs identification of transcription start sites and frequency of their usage from input CAGE sequencing data, normalization of raw CAGE tag count, clustering of TSSs into tag clusters (TC) and their aggregation across multiple CAGE experiments to construct the promoterome. It manipulates multiple CAGE experiments at once, performs expression profiling across experiments both at level of individual TSSs and clusters of TSSs and exports several different types of track files for visualization in the genome browser.
A reproducible clustering pipeline with multiple scales using capped analysis of gene expression (CAGE). RECLU discoveries numerous alternative transcription start sites (TSSs) with the biological implication for your sample.
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