├── .gitattributes ├── .github └── workflows │ ├── conventional-prs.yml │ ├── main.yml │ └── release-please.yml ├── .gitignore ├── .gitmodules ├── .snakemake-workflow-catalog.yml ├── .test ├── config │ ├── config.yaml │ ├── samples.tsv │ └── units.tsv ├── resources │ ├── gene_list.tsv │ ├── gene_list_2.tsv │ └── vega_volcano_plot.json └── three_prime │ ├── README.md │ ├── config │ ├── config.yaml │ ├── gene_sets.gmt │ ├── samples.tsv │ └── units.tsv │ └── workflow │ └── Snakefile ├── .travis.yml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── config ├── README.md ├── config.yaml ├── samples.tsv └── units.tsv ├── resources └── vega_volcano_plot.json └── workflow ├── Snakefile ├── envs ├── QC.yaml ├── biomart.yaml ├── biopython.yaml ├── canonical_reads.yaml ├── cpat.yaml ├── curl.yaml ├── enrichment.yaml ├── goatools.yaml ├── heatmap.yaml ├── hmmer.yaml ├── ihw.yaml ├── isoform-switch-analyzer.yaml ├── kallisto.yaml ├── pandas.yaml ├── pfam.yaml ├── polars.yaml ├── pysam.yaml ├── pystats.yaml ├── samtools.yaml ├── sleuth.yaml └── vega.yaml ├── report ├── diffexp-genes.rst ├── diffexp-representative.rst ├── diffexp.rst ├── diffsplice-plot.rst ├── diffsplice.rst ├── fastp.rst ├── fgsea-collapsed-table-plot.rst ├── fgsea-rank-ties.rst ├── fgsea-table-all.rst ├── fgsea-table-plot.rst ├── fgsea-table-significant.rst ├── go-enrichment-plot.rst ├── go-enrichment-sig_terms.rst ├── go-enrichment-table.rst ├── ihw-results.rst ├── logcount-matrix.rst ├── meta_compare.rst ├── plot-3prime-QC-histogram.rst ├── plot-adj-pvals-ihw.rst ├── plot-bootstrap.rst ├── plot-decision-ihw.rst ├── plot-dispersion-ihw.rst ├── plot-fgsea-gene-set.rst ├── plot-fld.rst ├── plot-group-density.rst ├── plot-heatmap.rst ├── plot-histograms-ihw.rst ├── plot-loadings.rst ├── plot-ma.rst ├── plot-mean-var.rst ├── plot-pc-variance.rst ├── plot-pca.rst ├── plot-pval-hist.rst ├── plot-qq.rst ├── plot-scatter.rst ├── plot-trends-ihw.rst ├── plot-vars.rst ├── plot-volcano.rst ├── samples.rst ├── spia.rst ├── units.rst └── workflow.rst ├── resources ├── custom_vega_plots │ ├── circle_diagram_genes.json │ ├── horizontal_bars.json │ └── waterfall_plot_study_items.json └── datavzrd │ ├── diffexp-template.yaml │ ├── go-enrichment-template.yaml │ ├── meta_comparison-diffexp-template.yaml │ ├── meta_comparison-go_terms-template.yaml │ ├── meta_comparison-pathways-template.yaml │ ├── samples-template.yaml │ ├── spia-template.yaml │ └── units-template.yaml ├── rules ├── bam.smk ├── common.smk ├── datavzrd.smk ├── diffexp.smk ├── diffsplice.smk ├── enrichment.smk ├── meta_comparisons.smk ├── qc_3prime.smk ├── quant.smk ├── quant_3prime.smk ├── ref.smk ├── ref_3prime.smk └── trim.smk ├── schemas ├── config.schema.yaml ├── samples.schema.yaml └── units.schema.yaml └── scripts ├── common.R ├── compare_diffexp.py ├── compare_enrichment.py ├── compare_pathways.py ├── compose-sample-sheet.py ├── ens_gene_to_go.R ├── fgsea.R ├── get-max-read-length.py ├── get-sample-hist-bins.py ├── get-spia-db.R ├── get-transcript-info.R ├── get_main_transcripts_per_gene_fasta.py ├── goatools-go-enrichment-analysis.py ├── ihw-fdr-control.R ├── isoform-switch-analysis-annotate.R ├── isoform-switch-analysis-init.R ├── plot-3prime-qc-histogram.py ├── plot-bootstrap.R ├── plot-diffexp-pval-hist.R ├── plot-fgsea-gene-sets.R ├── plot-fld.R ├── plot-group-density.R ├── plot-ind-sample-QC-histogram.py ├── plot-pca.py ├── plot-scatter.R ├── plot-unsupervised-heatmap.R ├── plot-variances.R ├── plot_diffexp_heatmap.R ├── plot_enrichment_pathway_scatter.py ├── postprocess_diffexp.py ├── postprocess_go_enrichment.py ├── postprocess_tpm.py ├── prepare-pca.R ├── remove_poly_tails.py ├── sleuth-diffexp.R ├── sleuth-init.R ├── sleuth-to-matrix.R ├── sleuth-to-tpm-matrix.R ├── spia.R └── vega_plot_volcano.py /.gitattributes: -------------------------------------------------------------------------------- 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