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Added pipeline 91b

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veghp 2019-09-13 16:33:04 +01:00
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@ -589,6 +589,12 @@ This repository contains tools for making web portals and interactive tools used
* line 5: a short line describing the data which will be included in the interactive page
* IMPORTANT NOTICE: if the vector partitioning the data (i.e. meta data column) is using integer indices (e.g. Louvain clustering which assigns integer identifies to clusters) it is highly recommended to pre-append the tag "Cluster\_" to all indices (e.g. "1" and "103" becomes "Cluster\_1" and "Cluster\_103" respectively). Failure to do so will not raise any errors, but the resulting interactive heatmap/dot plot will have glitches.
* A version of this script (91b) creates a html file from an csv file containing expression levels (columns: genes, rows: cell types; first datacell is empty). For this, the option file format is:
* line 1: expressions csv data filepath
* line 2: name of output folder
* line 3: name of interactive html page
* line 4: a short line describing the data
### pseudotime_webportal.sh
* see an example [here](https://developmentcellatlas.ncl.ac.uk/datasets/pseudotime_liver_blin/)
* this creates a web portal useful for exploring the results of a trajectory analysis