Detects probable locations for single-peak transcription start sites (TSSs) in a sequence. S-Peaker can acquire an UCSC custom track to visualize the probability of observing a single-peak TSS at every position of the sequence. This software is based on a method that identify TSS with the positional sequence features. Transcriptions revealed by strong single peak show that their locations can be mediated by position-specific sequences features.
A coordinated set of pipelines, 'piPipes', to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq. piPipes can also produce figures and tables suitable for publication. By facilitating data analysis, piPipes provides an opportunity to standardize computational methods in the piRNA field.
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.
A straightforward annotation-agnostic computational pipeline that greatly increases confidence in predicted transcription start sites (TSSs) and allows tuning by the end-user to balance both precision and sensitivity of TSS identification to address experimental needs. We provide an analysis of gene coverage and reproducibility, comparisons to previous work, and a software implementation for identification of high confidence TSSs.
Allows identification of transcription start sites (TSSs) and predicted enhancers. CAGEfightR is an R package that was developed for analyzing RNA-Seq, ChIP-Seq and microarrays available for Cap Analysis of Gene Expression (CAGE) analysis. It offers enhancer prediction, methods for robust tag clustering, annotation and visualization. This method can be used on datasets ranging from small-scale experiments to consortia-level projects.
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