junctionCounts 1.0.0-20240207-foss-2023a

junctionCounts (https://doi.org/10.1093/nargab/lqae093) is a tool intended to identify and quantify binary alternative splicing events from RNA-seq data. junctionCounts currently consists of two primary utilities: infer_pairwise_events.py, which identifies binary alternative splicing events (e.g. skipped exon events), and junctionCounts.py, which quantifies those events (i.e. provides a percent-spliced-in, or PSI value) from RNA-seq data (specifically from a BAM file).

Accessing junctionCounts 1.0.0-20240207-foss-2023a

To load the module for junctionCounts 1.0.0-20240207-foss-2023a please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load bear-apps/2023a
module load junctionCounts/1.0.0-20240207-foss-2023a

BEAR Apps Version

2023a

Architectures

EL8-icelake — EL8-sapphirerapids

The listed architectures consist of two parts: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

Extensions

• junctionCounts-1.0.0-20240207
• ncls 0.0.68

More Information

For more information visit the junctionCounts website.

Dependencies

This version of junctionCounts has a direct dependency on: BEDTools/2.31.1-GCC-12.3.0 cds_insertion/0.1dev-20240521-foss-2023a DEXSeq/1.50.0-foss-2023a-R-4.4.1 foss/2023a Pysam/0.22.0-GCC-12.3.0 Python/3.11.3-GCCcore-12.3.0 R/4.4.1-gfbf-2023a R-bundle-Bioconductor/3.19-foss-2023a-R-4.4.1 R-bundle-CRAN/2024.06-foss-2023a SciPy-bundle/2023.07-gfbf-2023a splice_lib/0.1dev-20240207-gfbf-2023a

Last modified on 12th March 2025