t-SNE is a popular dimensionality reduction method for, among many other things, identifying transcriptional subpopulations from single-cell RNA-seq data. However, the sensitivities of results to and the appropriateness of different parameters used have not been thoroughly investigated. Building on previously developed Javascript-based implementations of the t-SNE algorithm, we present this user-friendly web tool to begin to interactively explore the impact of these parameters on identified subpopulations.
To use your own data, paste your data into the datatable in the format shown with the sample demo data. Specifically, your data must be arranged with cells as rows and genes as columns in order to cluster on the cells. The first row of the datatable will be used as a header. Data values inputted into the first row will be disregarded. Similarly, the first two columns of the datatable will be used as cell names and cell annotations (to color the tSNE plot). If cell annotations are not available, this column can be kept empty. Data values inputted into the first two columns will be disregarded. All other entries must be numeric as they are assumed to be gene expression values.
Non-numeric entries such as NAs and Infs will result in errors.
You can Ctrl-A and Delete the datatable to clear the current sample demo data prior to pasting in your own data.
Error messages are available in the web console.
This webtool runs using your own computer's memory. In order to avoid crashing your own browser, please do not use this webtool with large datasets. Datasets should be subsetted to fewer than 100 genes AND fewer than 500 cells if possible. For more substantial analyses, please consult a bioinformatics collaborator.
THE WEBTOOL IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE WEBTOOL OR THE USE OR OTHER DEALINGS IN THE WEBTOOL.