Isosceles_Paper 0.2.0

Isosceles_Paper 0.2.0 release

Changes since commit 46ce788 (Nov 2, 2023):

• Updated the simulated bulk RNA-Seq analysis Jupyter notebook
  • Isosceles benchmark metrics have been updated to reflect the changes in Isosceles package
  • Added overall sensitivity, F1 score and precision plots
  • Fixed the ground truth expression percentile scale for FDR plots to match the TPM values used in other plots
• Updated the scripts for running Isosceles to reflect the changes in the package
• Nanopore bulk RNA-Seq and scRNA-Seq data benchmarks
  • Added Nanopore bulk vs pseudo bulk data benchmark reports for different numbers of top highly variable transcripts and their summary report
  • Updated the RMarkdown reports to make the barplot scale start at zero
  • Added new code and reports to benchmark Isosceles on Sicelore and wf-single-cell workflow input
• Simulated ovarian cell line data benchmarks
  • Added information on simulating ovarian cell line data to the input_data/ directory
  • Added the analysis directory (simulated_ovarian_analysis/) and RMarkdown reports for simulated ovarian cell line data benchmarks
• Added the analysis directory (sirv_analysis/) and RMarkdown report for SIRV data benchmarks
• Added the analysis directory (sequin_analysis/) and RMarkdown report for Sequin data benchmarks
• Added the analysis directory (pacbio_analysis/) and RMarkdown report for Pacbio, Nanopore and Illumina GM12878 data benchmarks
• Zenodo datasets
  • Updated the reference data dataset to include files used for for simulating ovarian cell line data
  • Updated the simulated bulk RNA-Seq report data dataset to include updated Isosceles de novo detection results
  • Updated the Nanopore scRNA-Seq report data dataset to include wf-single-cell workflow results
  • Uploaded simulated ovarian cell line data (FASTQ and BAM files)
  • Uploaded report data for the new benchmarks (e.g. SIRV or Sequin data)
  • Uploaded a new Singularity image for the current release of Isosceles
• Added a report for resource usage benchmarks on 5 million IGROV-1 Promethion reads to the reports_static/ directory
• Added a Jupyter notebook for simulated bulk RNA-Seq analysis using output from IsoQuant's first run to the reports_static/ directory
• Updated the Benchmark_commands.md file to include the information on running wf-single-cell workflow and aligning Pacbio reads
• Added selected NanoSim read model files to the input_data/ directory
• Added the YAML file for the isosceles_umitools conda environment to the software/ directory
• Minor fixes (typos, removed obsolete R packages loaded by the scripts etc.)