data/README.md

In lkmklsmn/empty_nn: Remove empty droplets in scRNA-seq data

Cell hashing dataset (Stoeckius et al)

The raw cell hashing datasets can be downloaded from paper or GSE108313. The RData file used in our analysis can be downloaded from google drive. It contains both the count matrix and label for each barcode.

Multiplexed PBMC dataset (Kang et al)

The raw bam file was downloaded from SRA website. More information can be found in SRR5398237. We used "bamtofastq" tool to generate appropriate formatted fastq files and then re-run cellranger 2.0 to get the raw count matrix, which can be downloaded from google drive. To run the Demuxlet, the merged VCF file from 32 individuals was downloaded from demuxlet github. We extracted the variants from the sequenced eight individuals.

snRNA-seq data from adult mouse brain

The raw 10x mouse brain scRNA-seq dataset was downloaded from https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/nuclei_2k

PBMC 8k dataset

The raw 10x PBMC 8k dataset (cellranger 2.1.0) was downloaded from https://cf.10xgenomics.com/samples/cell-exp/2.1.0/pbmc8k/pbmc8k_raw_gene_bc_matrices_h5.h5. Detailed information can be found in 10x PBMC_8k dataset_page.

Neuron 900 dataset

The raw 10x Neuron 900 dataset (cellranger 2.1.0) was downloaded from http://cf.10xgenomics.com/samples/cell-exp/2.1.0/neurons_900/neurons_900_raw_gene_bc_matrices_h5.h5. Detailed information can be found in 10x Neuron_900 dataset_page.

lkmklsmn/empty_nn documentation built on Jan. 30, 2024, 1:31 a.m.