├── .gitignore ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── analysis_scripts ├── alignment │ ├── README.md │ ├── RNACocktail-Alignment-Analysis.ipynb │ └── RNACocktail-Alignment-Analysis.py ├── denovo │ ├── README.md │ ├── RNACocktail-Denovo-Analysis.ipynb │ └── RNACocktail-Denovo-Analysis.py ├── diff │ ├── README.md │ ├── RNACocktail-DIFF-Analysis.ipynb │ └── RNACocktail-DIFF-Analysis.py ├── editing │ ├── README.md │ ├── RNACocktail-Editing-Analysis.ipynb │ └── RNACocktail-Editing-Analysis.py ├── fusion │ ├── README.md │ ├── RNACocktail-Fusion-Analysis.ipynb │ └── RNACocktail-Fusion-Analysis.py ├── quantification │ ├── README.md │ ├── RNACocktail-Quant-Analysis.ipynb │ └── RNACocktail-Quant-Analysis.py ├── reconstruction │ ├── README.md │ ├── RNACocktail-Reconstruction-Analysis.ipynb │ └── RNACocktail-Reconstruction-Analysis.py └── variant │ ├── README.md │ ├── RNACocktail-Variant-Analysis.ipynb │ └── RNACocktail-Variant-Analysis.py ├── docker └── Dockerfile ├── ez_setup.py ├── index.html ├── scripts ├── gpd2gtf.py ├── hisat2_jun2bed.py └── run_rnacocktail.py ├── setup.py ├── src ├── __init__.py ├── _version.py ├── defaults.py ├── external_cmd.py ├── main.py ├── run_diff.py ├── run_dnv_assemebly.py ├── run_editing.py ├── run_fusion.py ├── run_lr_align.py ├── run_lr_correct.py ├── run_lr_fusion.py ├── run_lr_reconstruct.py ├── run_quantify.py ├── run_reconstruct.py ├── run_sr_align.py ├── run_variant.py └── utils.py └── test ├── A1_1.fq.gz ├── A1_2.fq.gz ├── A2_1.fq.gz ├── A2_2.fq.gz ├── B1_1.fq.gz ├── B1_2.fq.gz ├── B2_1.fq.gz ├── B2_2.fq.gz ├── C_long.fa.gz ├── C_short.fa.gz ├── C_short_1.fq.gz ├── C_short_2.fq.gz ├── GRCh37_genes_pos.bed.gz ├── GRCh37_strand_pos.bed.gz ├── GRCh38.21.gpd.gz ├── GRCh38_genes_pos.bed.gz ├── GRCh38_strand_pos.bed.gz ├── docker_test.sh ├── hg19.known.21.gpd.gz └── test_run.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/README.md -------------------------------------------------------------------------------- /analysis_scripts/alignment/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/alignment/README.md -------------------------------------------------------------------------------- /analysis_scripts/alignment/RNACocktail-Alignment-Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/alignment/RNACocktail-Alignment-Analysis.ipynb -------------------------------------------------------------------------------- /analysis_scripts/alignment/RNACocktail-Alignment-Analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/alignment/RNACocktail-Alignment-Analysis.py -------------------------------------------------------------------------------- /analysis_scripts/denovo/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/denovo/README.md -------------------------------------------------------------------------------- /analysis_scripts/denovo/RNACocktail-Denovo-Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/denovo/RNACocktail-Denovo-Analysis.ipynb -------------------------------------------------------------------------------- /analysis_scripts/denovo/RNACocktail-Denovo-Analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/denovo/RNACocktail-Denovo-Analysis.py -------------------------------------------------------------------------------- /analysis_scripts/diff/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/diff/README.md -------------------------------------------------------------------------------- /analysis_scripts/diff/RNACocktail-DIFF-Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/diff/RNACocktail-DIFF-Analysis.ipynb -------------------------------------------------------------------------------- /analysis_scripts/diff/RNACocktail-DIFF-Analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/diff/RNACocktail-DIFF-Analysis.py -------------------------------------------------------------------------------- /analysis_scripts/editing/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/editing/README.md -------------------------------------------------------------------------------- /analysis_scripts/editing/RNACocktail-Editing-Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/editing/RNACocktail-Editing-Analysis.ipynb -------------------------------------------------------------------------------- /analysis_scripts/editing/RNACocktail-Editing-Analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/editing/RNACocktail-Editing-Analysis.py -------------------------------------------------------------------------------- /analysis_scripts/fusion/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/fusion/README.md -------------------------------------------------------------------------------- /analysis_scripts/fusion/RNACocktail-Fusion-Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/fusion/RNACocktail-Fusion-Analysis.ipynb -------------------------------------------------------------------------------- /analysis_scripts/fusion/RNACocktail-Fusion-Analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/fusion/RNACocktail-Fusion-Analysis.py -------------------------------------------------------------------------------- /analysis_scripts/quantification/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/quantification/README.md -------------------------------------------------------------------------------- /analysis_scripts/quantification/RNACocktail-Quant-Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/quantification/RNACocktail-Quant-Analysis.ipynb -------------------------------------------------------------------------------- /analysis_scripts/quantification/RNACocktail-Quant-Analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/quantification/RNACocktail-Quant-Analysis.py -------------------------------------------------------------------------------- /analysis_scripts/reconstruction/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/reconstruction/README.md -------------------------------------------------------------------------------- /analysis_scripts/reconstruction/RNACocktail-Reconstruction-Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/reconstruction/RNACocktail-Reconstruction-Analysis.ipynb -------------------------------------------------------------------------------- /analysis_scripts/reconstruction/RNACocktail-Reconstruction-Analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/reconstruction/RNACocktail-Reconstruction-Analysis.py -------------------------------------------------------------------------------- /analysis_scripts/variant/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/variant/README.md -------------------------------------------------------------------------------- /analysis_scripts/variant/RNACocktail-Variant-Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/variant/RNACocktail-Variant-Analysis.ipynb -------------------------------------------------------------------------------- /analysis_scripts/variant/RNACocktail-Variant-Analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/analysis_scripts/variant/RNACocktail-Variant-Analysis.py -------------------------------------------------------------------------------- /docker/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/docker/Dockerfile -------------------------------------------------------------------------------- /ez_setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/ez_setup.py -------------------------------------------------------------------------------- /index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/index.html -------------------------------------------------------------------------------- /scripts/gpd2gtf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/scripts/gpd2gtf.py -------------------------------------------------------------------------------- /scripts/hisat2_jun2bed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/scripts/hisat2_jun2bed.py -------------------------------------------------------------------------------- /scripts/run_rnacocktail.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/scripts/run_rnacocktail.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/setup.py -------------------------------------------------------------------------------- /src/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/__init__.py -------------------------------------------------------------------------------- /src/_version.py: -------------------------------------------------------------------------------- 1 | __version__ = "0.3.2" 2 | -------------------------------------------------------------------------------- /src/defaults.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/defaults.py -------------------------------------------------------------------------------- /src/external_cmd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/external_cmd.py -------------------------------------------------------------------------------- /src/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/main.py -------------------------------------------------------------------------------- /src/run_diff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_diff.py -------------------------------------------------------------------------------- /src/run_dnv_assemebly.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_dnv_assemebly.py -------------------------------------------------------------------------------- /src/run_editing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_editing.py -------------------------------------------------------------------------------- /src/run_fusion.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_fusion.py -------------------------------------------------------------------------------- /src/run_lr_align.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_lr_align.py -------------------------------------------------------------------------------- /src/run_lr_correct.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_lr_correct.py -------------------------------------------------------------------------------- /src/run_lr_fusion.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_lr_fusion.py -------------------------------------------------------------------------------- /src/run_lr_reconstruct.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_lr_reconstruct.py -------------------------------------------------------------------------------- /src/run_quantify.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_quantify.py -------------------------------------------------------------------------------- /src/run_reconstruct.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_reconstruct.py -------------------------------------------------------------------------------- /src/run_sr_align.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_sr_align.py -------------------------------------------------------------------------------- /src/run_variant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/run_variant.py -------------------------------------------------------------------------------- /src/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/src/utils.py -------------------------------------------------------------------------------- /test/A1_1.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/A1_1.fq.gz -------------------------------------------------------------------------------- /test/A1_2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/A1_2.fq.gz -------------------------------------------------------------------------------- /test/A2_1.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/A2_1.fq.gz -------------------------------------------------------------------------------- /test/A2_2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/A2_2.fq.gz -------------------------------------------------------------------------------- /test/B1_1.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/B1_1.fq.gz -------------------------------------------------------------------------------- /test/B1_2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/B1_2.fq.gz -------------------------------------------------------------------------------- /test/B2_1.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/B2_1.fq.gz -------------------------------------------------------------------------------- /test/B2_2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/B2_2.fq.gz -------------------------------------------------------------------------------- /test/C_long.fa.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/C_long.fa.gz -------------------------------------------------------------------------------- /test/C_short.fa.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/C_short.fa.gz -------------------------------------------------------------------------------- /test/C_short_1.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/C_short_1.fq.gz -------------------------------------------------------------------------------- /test/C_short_2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/C_short_2.fq.gz -------------------------------------------------------------------------------- /test/GRCh37_genes_pos.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/GRCh37_genes_pos.bed.gz -------------------------------------------------------------------------------- /test/GRCh37_strand_pos.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/GRCh37_strand_pos.bed.gz -------------------------------------------------------------------------------- /test/GRCh38.21.gpd.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/GRCh38.21.gpd.gz -------------------------------------------------------------------------------- /test/GRCh38_genes_pos.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/GRCh38_genes_pos.bed.gz -------------------------------------------------------------------------------- /test/GRCh38_strand_pos.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/GRCh38_strand_pos.bed.gz -------------------------------------------------------------------------------- /test/docker_test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/docker_test.sh -------------------------------------------------------------------------------- /test/hg19.known.21.gpd.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/hg19.known.21.gpd.gz -------------------------------------------------------------------------------- /test/test_run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioinform/rnacocktail/HEAD/test/test_run.sh --------------------------------------------------------------------------------