Published September 8, 2019 | Version 1.0

Workflow Open

Code for producing the analysis in the "Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq"

Creators: Valentine Svensson¹; Eduardo da Veiga Beltrame¹; Lior Pachter¹

1. California Institute of Technology

Description

Code for producing the analysis in the "Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq" by Valentine Svensson, Eduardo Beltrame and Lior Pachter

Files

README.md

Files (10.1 GB)

Name	Size	Actions
README.md md5:3c4bc5b22c91f6e20278f082ffd8a4c0	5.4 kB	Preview Download
cell-depth-tradeoff-metadata.tsv md5:bff01732f93bf27f38838df24a7e1e15	2.4 kB	Download
snakemake_subsampling_output.tar.gz md5:f587eff31bcc0796f848b03ed18c6555	3.2 GB	Download
heart10k_subsamples.h5ad md5:00920a38a8dc5608f77d65df793de142	1.7 GB	Download
neurons10k_clusters.csv md5:a15a1f1c585029c3df9c650c4c645200	251.7 kB	Preview Download
neurons10k_subsamples.h5ad md5:1c1894d603fc1e517382e768425772f6	2.5 GB	Download
pbmc10k_clusters.csv md5:be5b0560f192007a63b7a26b2a97f688	249.8 kB	Preview Download
1) cell-depth-tradeoff-subsampling.py md5:43424a71023c064cce97a6ca2af12d44	8.0 kB	Download
2) create_H5AD.ipynb md5:f55e877c4b01b5501b4b621bcb77a6bb	15.2 kB	Preview Download
pbmc10k_subsamples.h5ad md5:92420b8332121bb7e47ff09668540710	2.7 GB	Download
3) run_scvi.py md5:90b965aa7b3320e20a303a6addf90123	5.5 kB	Download
4) make_all_plots.ipynb md5:48ee82fda9264dea80c5ed9496ff3254	8.4 MB	Preview Download
scvi_output_all_datasets.tar.gz md5:3b31cc98cc905961bf18b26d701eb421	51.0 MB	Download
heart10k_clusters.csv md5:f995c9b48a9c108fc5c6c053da23043c	163.0 kB	Preview Download

Additional details

DOI

Resource type: Workflow
Publisher: CaltechDATA
Languages: English
Formats: csv, py, ipynb, h5ad

Created:: September 9, 2022
Modified:: November 28, 2022