jjriley1

PhD Student at The University of Sheffield. Member of @sudlab.

Sheffield, UK

Pinned Repositories

pipeline_3UI_saturation
Pipeline to assess saturation of 3UI detection
Language:Python00
pipeline_DTU
Pipeline to determine differential transcript usage (DTU) from RNA-sequencing data and detects flips in isoform expression between experimental conditions.
Language:Python00
pipeline_fastqc
Pipeline to download raw sequencing read data in .fastq format from .remote files given as inputs and run quality control on them. Sourced from sudlab shared network at The University of Sheffield.
Language:Python00
pipeline_QAPA
Pipeline to detect the occurrence of differential alternative polyadenylation (APA) between sets of RNA-sequencing reads from different experimental conditions
Language:Python00
pipeline_rMATS
Pipeline to detect differential alternative splicing from RNA-sequencing data by using the rMATS software.
Language:Python00
pipeline_utrons
Pipeline to detect 3'UTR introns (3UIs or "utrons") and quantify their expression in RNA-sequencing data. Pipeline forked from sudlab/pipeline_utrons to use newer version of Salmon and incorporate decoy-aware transcriptome indexing.
Language:Python00
process_qPCRs
Pipeline used in the analysis of qPCR data between 3'UTR intron splicing and retaining isoforms.
Language:Python00
Cancer3UIs
Repository for code related to cancer 3UIs paper
Language:HTML00

jjriley1/pipeline_3UI_saturation
Pipeline to assess saturation of 3UI detection
Language:Python
jjriley1/process_qPCRs
Pipeline used in the analysis of qPCR data between 3'UTR intron splicing and retaining isoforms.
Language:Python
jjriley1/pipeline_rMATS
Pipeline to detect differential alternative splicing from RNA-sequencing data by using the rMATS software.
Language:Python
jjriley1/pipeline_DTU
Pipeline to determine differential transcript usage (DTU) from RNA-sequencing data and detects flips in isoform expression between experimental conditions.
Language:Python
jjriley1/pipeline_QAPA
Pipeline to detect the occurrence of differential alternative polyadenylation (APA) between sets of RNA-sequencing reads from different experimental conditions
Language:Python
jjriley1/pipeline_fastqc
Pipeline to download raw sequencing read data in .fastq format from .remote files given as inputs and run quality control on them. Sourced from sudlab shared network at The University of Sheffield.
Language:Python
jjriley1/pipeline_utrons
Pipeline to detect 3'UTR introns (3UIs or "utrons") and quantify their expression in RNA-sequencing data. Pipeline forked from sudlab/pipeline_utrons to use newer version of Salmon and incorporate decoy-aware transcriptome indexing.