This is an R data package that contains pre-processed single cell data in formats expected by scpcaTools.
Data are processed with alevin-fry, kallisto bustools and cellranger, using workflows from https://github.com/AlexsLemonade/alsf-scpca/tree/main/workflows
Sample data used is from a small 10X Genomics sample data set for invasive ductal carcinoma, available for download from the 10X website: https://support.10xgenomics.com/single-cell-gene-expression/datasets/6.0.0/Breast_Cancer_3p_LT
Description from 10X website
750 Sorted Cells from Human Invasive Ductal Carcinoma, 3’ LT v3.1
Single Cell Gene Expression Dataset by Cell Ranger 6.0.0
Invasive Ductal Carcinoma cells from a female donor aged 65 were obtained by 10x Genomics from Discovery Life Sciences.Libraries were prepared following the Chromium Next GEM Single Cell 3' LT Reagent Kits v3.1 (Dual Index) User Guide (CG000399) and sequenced on Illumina NovaSeq 6000.
Sequencing Depth: 62,379 mean reads per cell
Paired-end, dual indexing Read 1: 28 cycles (16 bp barcode, 12 bp UMI) i5 index: 10 cycles (sample index) i7 index: 10 cycles (sample index) Read 2: 90 cycles (transcript)This dataset is licensed under the Creative Commons Attribution license.