Algorithm and scientific questions: <Huidong.Chen at mgh dot harvard dot edu>
Module wrapping issues: Ted Liefeld < jliefeld at cloud dot ucsd dot edu>
STREAM (Single-cell Trajectories Reconstruction, Exploration And Mapping) is an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. Within GenePattern STREAM is implemented as a collection of modules that cover the entire STREAM processing pipeline to allow individual steps to be performed interactively for data exploration.
STREAM.DetectLeafGenes is used to detect marker genes for each leaf branch.
For each gene E we scale the gene expression values to [0,1]. Then we calculate the average gene expressions for all leaf branches. Based on the average expressions, we calculate the Z-scores of all leaf branches. If there is any leaf branch with an absolute Z-score greater than 1.5, then the leaf branch with the highest absolute Z-score value will be picked as the candidate leaf branch. Next, Kruskal–Wallis H-test is computed for all the leaf branches to test if a significant difference of gene expression median value between leaf branches exists. If it is significant (p-value < 0.01), then a post-hoc pairwise Conover’s test is computed for multiple comparisons of mean rank sums test between all leaf branches. If the p-values between the candidate leaf branch and the other leaf branches are all below the specified threshold (0.01), then the gene E will be considered as leaf gene of the candidate leaf branch.
H Chen, L Albergante, JY Hsu, CA Lareau, GL Bosco, J Guan, S Zhou, AN Gorban, DE Bauer, MJ Aryee, DM Langenau, A Zinovyev, JD Buenrostro, GC Yuan, L Pinello Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nature Communications, volume 10, Article number: 1903 (2019)
Nestorowa, S. et al. A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. Blood 128, e20-31 (2016).
Pinello Lab STREAM Github Repository
Example data for the STREAM workflow can be downloaded from dropbox: Stream Example Data
Ref: Nestorowa, S. et al. A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. Blood 128, e20-31 (2016).
Example data for this specific step can be found at stream_epg_result.pkl
GenePattern 3.9.11 or later (dockerized).
Inputs and Outputs
|data file*||A STREAM pkl file containing an annotated AnnData matrix of gene expression data/td>|
|output filename*||The output filename prefix.|
Marker Gene DetectionParameters used if variable genes are to be selected as the feature.
|root||The starting node.|
|preference||The preference of nodes. The branch with speficied nodes are preferred and put on the top part of subway plot. The higher ranks the node have, the closer to the top the branch with that node is. e.g. S3,S4.|
|percentile expr*||Between 0 and 100. Between 0 and 100. Specify the percentile of gene expression greater than 0 to filter out some extreme gene expressions.|
|use precomputed*||If True, the previously computed scaled gene expression will be used.|
|cutoff zscore*||The z-score cutoff used for mean values of all leaf branches.|
|cutoff pvalue||The p value cutoff used for Kruskal-Wallis H-test and post-hoc pairwise Conover's test.|
* - required