single-cell-3prime-paper

single-cell-3prime-paper copied to clipboard

Hello! I have been using the FACS-sorted PBMC cells from the Zheng et al 2017 paper. But returning to the link provided here (and in the article) directs me to...

Chibuikem709

Cluster labels missing, and where to find annotations for 68K PBMC?

7

Hi, I'm looking for annotations for the 68K PBMC dataset that corresponds to Fig 3 in Zheng et al. I downloaded the kmeans clustering labels for the 68K PBMCs from...

lynnyi

Missing Files

1

It seems that the links to the files pbmc68k_data.rds, all_pure_pbmc_data.rds (1.5GB) and all_pure_select_11types.rds are broken, and that they are no longer on the 10x Genomics site? Is there anywhere else...

ChristopherSerody

.plot_heatmap_and_write_genes(n_clust=10, tsne_df=tdf_n_1000, mat=m_n_1000, genes=use_genes_n_id[1:1000], dir=file.path(RES_DIR,"k10_marker_genes.tsv")) markers

DebbieCG

to prevent error.

yasinkaymaz

downsample_gene_bc_mtx function error

3

This might be a system incompatability, but when I try to ran the code, it gave me an error about bc_gene_umi_subsampled not being a data table. Adding the setDT function...

chenlingantelope

There is a name conflict between the actual pipeline and the util: `.plot_heatmap_and_write_genes` is called in pipeline (See [here](https://github.com/10XGenomics/single-cell-3prime-paper/blob/265433ebf858c7fdcab759ca9f36b5e0241ceece/pbmc68k_analysis/main_process_68k_pbmc.R#L92-L93)) while it was implemented as `plot_heatmap_and_write_genes` without the first dot (See...

Puriney