On this page, we make some of the raw data files available for conducting your own analyses.
Here are links to all of the data used in the tutorial (code is presented for downloading and processing these files through the course of the tutorial too).
| Name | Last modified | Size | Description |
|---|---|---|---|
| irlba_1.0.3.tar.gz | 18-Nov-2017 17:20 | 177K | Source code for irlba version 1.0.3, the version used for latent semantic indexing in Cusanovich, Reddington, Garfield et al. |
| monocle_2.3.5.tar.gz | 18-Nov-2017 17:20 | 16M | Source code for Monocle version 2.3.5, the version used for pseudotemporal ordering in Cusanovich, Reddington, Garfield et al. |
| DDRTree_0.1.4.tar.gz | 16-Jan-2018 11:23 | 12K | Source code for DDRTree version 0.1.4, the version used for pseudotemporal ordering in Cusanovich, Reddington, Garfield et al. |
| monocle_patch.R | 18-Nov-2017 17:20 | 6.6K | A small update to Monocle that causes the differentialGeneTest to return beta values. |
| 6to8.2kbmatrix.sparse.binary.rds | 18-Nov-2017 17:20 | 113M | A binary matrix recording whether insertions were observed in 2kb windows throughout the genome in all 6-8 hour cells. This file is provided as a sparse matrix in .rds format so that it can be easily loaded into R. |
| 6to8.summitmatrix.sparse.binary.rds | 18-Nov-2017 17:19 | 69M | A binary matrix recording whether insertions were observed in a master list of potential regulatory elements in all 6-8 hour cells. This file is provided as a sparse matrix in .rds format so that it can be easily loaded into R. |
| 6to8.xycalls.txt | 18-Nov-2017 17:19 | 300K | A file assigning a sex to each cell from the 6-8 hour time point on the basis of reads mapping to the sex chromosomes. A 1 indicates male and a 2 indicates female. |
| 6to8.read.report.txt | 18-Nov-2017 17:19 | 429K | A file reporting the total number of unique reads recovered from each cell. This was used in the logistic regression analysis to control for cells having varying complexity. |
| 2to4_files.tar.gz | 18-Nov-2017 17:19 | 44M | A tarball of all the files required for pseudotemporal ordering of cells from the 2-4 hour time point. |