--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu Jul 18 11:13:41 2019 -0400
@@ -0,0 +1,84 @@
+# Wrappers for Scater
+
+This code wraps a number of [scater](https://bioconductor.org/packages/release/bioc/html/scater.html) functions as Galaxy wrappers. Briefly, the `scater-create-qcmetric-ready-sce` tool takes a sample gene expression matrix (usually read-counts) and a cell annotation file, creates a [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) object and runs scater's `calculateQCMetrics` function (using other supplied files such as ERCC's and mitochondrial gene features).
+Various filter scripts are provided, along with some plotting functions for QC.
+
+
+## Typical workflow
+
+1. Read in data with `scater-create-qcmetric-ready-sce`.
+2. Visualise it.\
+   Take a look at the distribution of library sizes, expressed features and mitochondrial genes with `scater-plot-dist-scatter`.
+   Then look at the distibution of genes across cells with `scater-plot-exprs-freq`.
+3. Guided by the plots, filter the data with `scater-filter`.\
+   You can either manually filter with user-defined parameters or use PCA to automatically removes outliers.
+4. Visualise data again to see how the filtering performed using `scater-plot-dist-scatter`.\
+   Decide if you're happy with the data. If not, try increasing or decreasing the filtering parameters.
+5. Normalise data with `scater-normalize`.
+6. Investigate other confounding factors.\
+   Plot the data (using PCA) and display various annotated properties of the cells using `scater-plot-pca`.
+
+## Command-line usage
+
+For help with any of the following scripts, run:
+ `<script-name> --help`
+
+---
+
+`scater-create-qcmetric-ready-sce.R`
+Takes an expression matrix (usually read-counts) of samples (columns) and gene/transcript features (rows), along with other annotation information, such as cell metadata, control genes (mitochondrail genes, ERCC's), creates a [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) object and runs scater's `calculateQCMetrics`. Save the resulting SingleCellExperiment object in Loom format.
+
+
+```
+./scater-create-qcmetric-ready-sce.R -a test-data/counts.txt -c test-data/annotation.txt -f test-data/mt_controls.txt  -o test-data/scater_qcready.loom
+```
+
+---
+
+`scater-plot-dist-scatter.R`
+Takes SingleCellExperiment object (from Loom file) and plots a panel of read and feature graphs, including the distribution of library sizes, distribution of feature counts, a scatterplot of reads vs features, and % of mitochondrial genes in library.
+
+```
+./scater-plot-dist-scatter.R -i test-data/scater_qcready.loom -o test-data/scater_reads_genes_dist.pdf
+```
+
+---
+
+`scater-plot-exprs-freq.R`
+Plots mean expression vs % of expressing cells and provides information as to the number of genes expressed in 50% and 25% of cells.
+
+---
+
+`scater-pca-filter.R`
+Takes SingleCellExperiment object (from Loom file) and automatically removes outliers from data using PCA. Save the filtered SingleCellExperiment object in Loom format.
+
+```
+./scater-pca-filter.R -i test-data/scater_qcready.loom -o test-data/scater_pca_filtered.loom
+```
+
+---
+
+`scater-manual-filter.R`
+Takes SingleCellExperiment object (from Loom file) and filters data using user-provided parameters. Save the filtered SingleCellExperiment object in Loom format.
+
+```
+./scater-manual-filter.R -i test-data/scater_qcready.loom -l 10000 -d 4 -m 33 -o test-data/scater_manual_filtered.loom
+```
+
+---
+
+`scater-normalize.R`
+Compute log-normalized expression values from count data in a SingleCellExperiment object, using the size factors stored in the object. Save the normalised SingleCellExperiment object in Loom format.
+
+```
+./scater-normalize.R -i test-data/scater_manual_filtered.loom -o test-data/scater_man_filtered_normalised.loom
+```
+
+---
+
+`scater-plot-pca.R`
+PCA plot of a normalised SingleCellExperiment object (produced with `scater-normalize.R`). The options `-c`, `-p`, and `-s` all refer to cell annotation features. These are the column headers of the `-c` option used in `scater-create-qcmetric-ready-sce.R`.
+
+```
+./scater-plot-pca.R -i test-data/scater_man_filtered_normalised.loom -c Treatment -p Mutation_Status -o test-data/scater_pca_plot.pdf
+```