├── LICENSE ├── README.md ├── example_dataset ├── 10xGet_cell_barcodes_hgmm_small.ipynb ├── 10xResults_hgmm_small.ipynb ├── config.json └── fastq_files │ ├── read-I1_si-ATCGCTCC_lane-001-chunk-001.fastq.tst.gz │ ├── read-I1_si-ATCGCTCC_lane-002-chunk-000.fastq.tst.gz │ ├── read-I1_si-CCGTACAG_lane-001-chunk-001.fastq.tst.gz │ ├── read-I1_si-CCGTACAG_lane-002-chunk-000.fastq.tst.gz │ ├── read-I1_si-GATAGGTA_lane-001-chunk-001.fastq.tst.gz │ ├── read-I1_si-GATAGGTA_lane-002-chunk-000.fastq.tst.gz │ ├── read-I1_si-TGACTAGT_lane-001-chunk-001.fastq.tst.gz │ ├── read-I1_si-TGACTAGT_lane-002-chunk-000.fastq.tst.gz │ ├── read-RA_si-ATCGCTCC_lane-001-chunk-001.fastq.tst.gz │ ├── read-RA_si-ATCGCTCC_lane-002-chunk-000.fastq.tst.gz │ ├── read-RA_si-CCGTACAG_lane-001-chunk-001.fastq.tst.gz │ ├── read-RA_si-CCGTACAG_lane-002-chunk-000.fastq.tst.gz │ ├── read-RA_si-GATAGGTA_lane-001-chunk-001.fastq.tst.gz │ ├── read-RA_si-GATAGGTA_lane-002-chunk-000.fastq.tst.gz │ ├── read-RA_si-TGACTAGT_lane-001-chunk-001.fastq.tst.gz │ └── read-RA_si-TGACTAGT_lane-002-chunk-000.fastq.tst.gz ├── hgmm ├── 10xGet_cell_barcodes_hgmm.ipynb └── 10xResults_hgmm.ipynb ├── notebooks ├── 10xGet_cell_barcodes.ipynb └── 10xResults.ipynb ├── pbmc3k ├── 10xGet_cell_barcodes_pbmc3k.ipynb └── 10xResults_pbmc3k.ipynb └── source ├── 10xDetect_and_Prep.py ├── 10xPrepData.py ├── compute_TCCs.py ├── error_correct_and_split.py ├── get_cell_barcodes.py └── prep_TCC_matrix.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/scRNA-Seq-TCC-prep/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pachterlab/scRNA-Seq-TCC-prep/HEAD/README.md -------------------------------------------------------------------------------- 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