densitypeakclusters.txt.gzfiles 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).
|irlba_1.0.3.tar.gz||18-Nov-2017 17:20||177K||Source code for
|monocle_2.3.5.tar.gz||18-Nov-2017 17:20||16M||Source code for
|DDRTree_0.1.4.tar.gz||16-Jan-2018 11:23||12K||Source code for
|monocle_patch.R||18-Nov-2017 17:20||6.6K||A small update to Monocle that causes the
|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
|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
|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
|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.
|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.
|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.
|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.|