06/09/2019 adds summitmatrix.sparse.binary.rds, tsnecoords.txt.gz, and densitypeakclusters.txt.gz files for all three timepoints.03/14/2018: Initial release.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. |
Here we make peak of accessibility by cell matrices for all three time points. Each matrix is a sparse matrix file in .rds format. Requires the Matrix package in R to open.
| Name | Last modified | Size | Description |
|---|---|---|---|
| 2to4.summitmatrix.sparse.binary.rds | 8-Jun-2019 07:05 | 59M | Accessiblity matrix for the 2-4hr timepoint. |
| 6to8.summitmatrix.sparse.binary.rds | 18-Nov-2017 17:19 | 69M | Accessiblity matrix for the 6-8hr timepoint. The same file is also available in the Tutorial section and is just reproduced here for consistency. |
| 10to12.summitmatrix.sparse.binary.rds | 9-Jun-2019 14:37 | 48M | Accessiblity matrix for the 10-12hr timepoint. |
Here we make t-SNE coordinates for each timepoint available. See the manuscript for how t-SNE coordinates were calculated. Each file is a gzipped .tsv and includes 3 columns: Cell ID column, x-axis coordinate column, y-axis coordinate column.
| Name | Last modified | Size | Description |
|---|---|---|---|
| 2to4.tsnecoords.txt.gz | 9-Jun-2019 15:12 | 165K | t-SNE coordinates for the 2-4hr timepoint. |
| 6to8.tsnecoords.txt.gz | 9-Jun-2019 15:12 | 162K | t-SNE coordinates for the 6-8hr timepoint. |
| 10to12.tsnecoords.txt.gz | 9-Jun-2019 15:12 | 149K | t-SNE coordinates for the 10-12hr timepoint. |
Here we make the density peak-based cluster assignments (derived from the t-SNE coordinates) for each timepoint available. See the manuscript for how t-SNE coordinates were calculated and how density peak clusters were identified. Each file is a gzipped .tsv and includes 2 columns: Cell ID column, cluster assignment.
| Name | Last modified | Size | Description |
|---|---|---|---|
| 2to4.densitypeakclusters.txt.gz | 8-Jun-2019 05:42 | 34K | Cluster assignments for the 2-4hr timepoint. |
| 6to8.densitypeakclusters.txt.gz | 8-Jun-2019 05:42 | 34K | Cluster assignments for the 6-8hr timepoint. |
| 10to12.densitypeakclusters.txt.gz | 8-Jun-2019 05:41 | 31K | Cluster assignments for the 10-12hr timepoint. |