LICENSE.md
MANIFEST.in
README.md
pyproject.toml
setup.py
SnakeAltPromoter.egg-info/PKG-INFO
SnakeAltPromoter.egg-info/SOURCES.txt
SnakeAltPromoter.egg-info/dependency_links.txt
SnakeAltPromoter.egg-info/entry_points.txt
SnakeAltPromoter.egg-info/requires.txt
SnakeAltPromoter.egg-info/top_level.txt
snakealtpromoter/_version.py
snakealtpromoter/cli.py
snakealtpromoter/data/Human_GSM4421328_Human_Left_Ventrice_Tissue_Healthy_cDNA_PAIRED_SRR11351704_R1.fastq.gz
snakealtpromoter/data/Human_GSM4421328_Human_Left_Ventrice_Tissue_Healthy_cDNA_PAIRED_SRR11351704_R2.fastq.gz
snakealtpromoter/data/Human_GSM4421329_Human_Left_Ventrice_Tissue_Healthy_cDNA_PAIRED_SRR11351705_R1.fastq.gz
snakealtpromoter/data/Human_GSM4421329_Human_Left_Ventrice_Tissue_Healthy_cDNA_PAIRED_SRR11351705_R2.fastq.gz
snakealtpromoter/data/Human_GSM4421331_Human_Left_Ventrice_Tissue_Heart_Failure_cDNA_PAIRED_SRR11351707_R1.fastq.gz
snakealtpromoter/data/Human_GSM4421331_Human_Left_Ventrice_Tissue_Heart_Failure_cDNA_PAIRED_SRR11351707_R2.fastq.gz
snakealtpromoter/data/Human_GSM4421332_Human_Left_Ventrice_Tissue_Heart_Failure_cDNA_PAIRED_SRR11351708_R1.fastq.gz
snakealtpromoter/data/Human_GSM4421332_Human_Left_Ventrice_Tissue_Heart_Failure_cDNA_PAIRED_SRR11351708_R2.fastq.gz
snakealtpromoter/data/hg38.fa
snakealtpromoter/data/hg38.gtf
snakealtpromoter/data/samplesheet/Heart_CAGE.tsv
snakealtpromoter/data/samplesheet/Heart_RNAseq.tsv
snakealtpromoter/data/samplesheet/samplesheet.tsv
snakealtpromoter/docs/Genomesetup.md
snakealtpromoter/docs/Snakealtpromoter.md
snakealtpromoter/docs/workflow_overview.png
snakealtpromoter/rules/Genomesetup.Snakefile
snakealtpromoter/rules/Snakealtpromoter.Snakefile
snakealtpromoter/rules/envs/altbasic.yaml
snakealtpromoter/rules/envs/altbasicR.yaml
snakealtpromoter/rules/envs/altbasicRlimma.yaml
snakealtpromoter/rules/envs/bam.yaml
snakealtpromoter/rules/envs/basic.yaml
snakealtpromoter/rules/envs/dexR.yaml
snakealtpromoter/rules/envs/featurecounts.yaml
snakealtpromoter/rules/envs/r.yaml
snakealtpromoter/scripts/CAGE_bam.R
snakealtpromoter/scripts/CAGE_count.R
snakealtpromoter/scripts/RNANEW_test_unchanged_plots_tsne_only.R
snakealtpromoter/scripts/compare_different_methods.R
snakealtpromoter/scripts/data_download.R
snakealtpromoter/scripts/dexseq_counts_separate.R
snakealtpromoter/scripts/get_strand.py
snakealtpromoter/scripts/merge_promoter_counts.R
snakealtpromoter/scripts/plots.R
snakealtpromoter/scripts/plots_total.R
snakealtpromoter/scripts/proactiv_count_merged.R
snakealtpromoter/scripts/proactiv_differential.R
snakealtpromoter/scripts/proactiv_prepare_promoter_annotation.R
snakealtpromoter/scripts/promoter_classify.R
snakealtpromoter/scripts/promoter_classify_total.R
snakealtpromoter/scripts/promoter_count.R
snakealtpromoter/scripts/promoter_differential.R
snakealtpromoter/scripts/salmon_counts.R
snakealtpromoter/scripts/sanity_check.R
snakealtpromoter/scripts/downstream_plots/Fig2
snakealtpromoter/scripts/downstream_plots/RPKM_length.R
snakealtpromoter/scripts/downstream_plots/Venn_major_minor.R
snakealtpromoter/scripts/downstream_plots/method_comparison_DEG_only.R
snakealtpromoter/scripts/downstream_plots/scatterplot.count.rpkm.R
snakealtpromoter/scripts/downstream_plots/scatterplot.de.R
snakealtpromoter/ui/__init__.py
snakealtpromoter/ui/launch.py
snakealtpromoter/ui/stl_app.py
snakealtpromoter/workflows/Genomesetup.py
snakealtpromoter/workflows/Snakealtpromoter.py
snakealtpromoter/workflows/__init__.py