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biotoolbox

Tools for querying and analysis of genomic data

growthcurveanalysis

intron_enrichment_score

The intronic enrichment score calculates the average coverage of RNA-seq reads over introns relative to neighboring exons in Saccharomyces cerevisiae. This score can be used to quantify enrichment of nascent transcripts from techniques such as 4tU-seq and TT-seq or to quantify defects in transcript splicing.

intronexon_junction_splice_ratio

Code and associated annotation file to count the ratio of spliced an unspliced reads for all intron-containing genes.

nucleosome_entry_exit_analysis_code

Source code for processing RNA-seq, ChIP-seq, and MNase-Seq data for Hildreth et al. "Mutations that alter the nucleosome DNA entry-exit site impair transcription termination in vivo"

rnaseq_analysis_code

This repository holds code for RNA-seq analysis handling stranded and un-stranded RNA-seq data.

spikeincorrectionfactor

Code related to calculating a corrective scaling factor to detect and correct for off-expecation ratios of sample to spike in for NGS experiments.