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Raw

scVI-reproducibility

Contact

romain [underscore] lopez [at] berkeley [dot] edu

Datasets

  • CORTEX

Original file expression_mRNA_17-Aug-2014.txt can be dowloaded here https://storage.googleapis.com/linnarsson-lab-www-blobs/blobs/cortex/expression_mRNA_17-Aug-2014.txt

  • PBMC

An additional R script to extract the quantity of interest from SCONE objects is needed (additional/PBMC.R) scVI_scone.rda, scone_all_wposcon_extendim_biostrat2_q.rda, molecule_qc_8k.txt, molecule_qc_4k.txt and gene_info.csv (containing the merged p-values from the microarray experiments) are in additional/data.zip

  • BRAIN LARGE

An additional Jupyter Notebook to format the data for scVI is needed (additional/BRAIN-LARGE.ipynb) 1M_neurons_filtered_gene_bc_matrices_h5.h5 can be downloaded here http://cf.10xgenomics.com/samples/cell-exp/1.3.0/1M_neurons/1M_neurons_filtered_gene_bc_matrices_h5.h5

  • RETINA

An additional R script, based on the original analysis is needed (additional/RETINA.R) We modified the file class.R so that the gene filtering also apply to the raw matrix, use ours in this repo (additional/class.R) The file bipolar_data_Cell2016.Rdata can be downloaded here https://github.com/broadinstitute/BipolarCell2016 The file ClustAssignFile.txt was obtained from the author, uploaded in additional/data.zip

  • HEMATO

Original files bBM.raw_umifm_counts.csv can be downloaded here https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2388072 bBM.spring_and_pba.csv and bBM.filtered_gene_list.paper.txt were sent by authors, uploaded in additional/data.zip

  • CBMC

Original files GSE100866_CBMC_8K_13AB_10X-RNA_umi.csv, GSE100866_CBMC_8K_13AB_10X-ADT_umi.csv, GSE100866_CBMC_8K_13AB_10X-ADT_clr-transformed.csv can be downloaded here https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866

  • BRAIN SMALL

Original files genes.tsv, barcodes.tsv, matrix.mtx and clusters.csv can be downloaded here https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/neuron_9k molecule_qc.txt was extracted from the original file http://cf.10xgenomics.com/samples/cell-exp/2.1.0/neuron_9k/neuron_9k_molecule_info.h5 using the additional python script additional/molecule_info.py (credit David Detomaso)

System requirements

  • Python 2.7.12 (version tested) or compatible
  • Tensorflow 1.3.0 (version tested) or compatible

Installation guide

  • Clone the github repository, install the dependencies and call functions from the modules scVI
  • Install time (< 10 min)

Demo

  • simply follow the given notebook
  • output should match the paper
  • run time should be less than 10 min on any hardware (including CPU, CORTEX is a small dataset)

Instructions

  • Follow the analysis notebooks