Alex Francette's repositories
IntronExon_Junction_Splice_Ratio
Code and associated annotation file to count the ratio of spliced an unspliced reads for all intron-containing genes.
biotoolbox
Tools for querying and analysis of genomic data
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.
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.