├── .gitignore ├── License.md ├── README.md ├── example ├── SRR1873277_1m_r1.fastq.gz └── SRR1873277_1m_r2.fastq.gz ├── notebooks ├── Evaluate_simulations.ipynb └── Inspect_sircel_kallisto.ipynb ├── setup.py └── sircel ├── Basic_pipeline.py ├── Sircel_master.py ├── Split_reads.py ├── __init__.py ├── __main__.py ├── params.json └── utils ├── Evaluate_cell_errors.py ├── Evaluate_simulations.py ├── Graph_utils.py ├── IO_utils.py ├── Logger.py ├── Plot_utils.py ├── Run_kallisto_tagged_bam.py ├── Simulate_multiple_datasets.py └── __init__.py /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | __pycache__/ 3 | 4 | -------------------------------------------------------------------------------- /License.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/License.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/README.md -------------------------------------------------------------------------------- /example/SRR1873277_1m_r1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/example/SRR1873277_1m_r1.fastq.gz -------------------------------------------------------------------------------- /example/SRR1873277_1m_r2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/example/SRR1873277_1m_r2.fastq.gz -------------------------------------------------------------------------------- /notebooks/Evaluate_simulations.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/notebooks/Evaluate_simulations.ipynb -------------------------------------------------------------------------------- /notebooks/Inspect_sircel_kallisto.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/notebooks/Inspect_sircel_kallisto.ipynb -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/setup.py -------------------------------------------------------------------------------- /sircel/Basic_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/Basic_pipeline.py -------------------------------------------------------------------------------- /sircel/Sircel_master.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/Sircel_master.py -------------------------------------------------------------------------------- /sircel/Split_reads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/Split_reads.py -------------------------------------------------------------------------------- /sircel/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/__init__.py -------------------------------------------------------------------------------- /sircel/__main__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/__main__.py -------------------------------------------------------------------------------- /sircel/params.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/params.json -------------------------------------------------------------------------------- /sircel/utils/Evaluate_cell_errors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/utils/Evaluate_cell_errors.py -------------------------------------------------------------------------------- /sircel/utils/Evaluate_simulations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/utils/Evaluate_simulations.py -------------------------------------------------------------------------------- /sircel/utils/Graph_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/utils/Graph_utils.py -------------------------------------------------------------------------------- /sircel/utils/IO_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/utils/IO_utils.py -------------------------------------------------------------------------------- /sircel/utils/Logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/utils/Logger.py -------------------------------------------------------------------------------- /sircel/utils/Plot_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/utils/Plot_utils.py -------------------------------------------------------------------------------- /sircel/utils/Run_kallisto_tagged_bam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/utils/Run_kallisto_tagged_bam.py -------------------------------------------------------------------------------- /sircel/utils/Simulate_multiple_datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/utils/Simulate_multiple_datasets.py -------------------------------------------------------------------------------- /sircel/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/sircel/HEAD/sircel/utils/__init__.py --------------------------------------------------------------------------------