README.md

Analyze Halo data

Step 1: Install

On MSK server, with R ```{r eval=FALSE} /home/byrne/R/R-3.4.3/bin/R

Run
```{r eval=FALSE}
library(devtools)
install_github("caitlinjones/halo")

Step 2: Create manifest with all project parameters

Example here

Step 3: Run pipeline or one step at a time

To generate counts and/or plots of Object Analysis data from Halo, run ```{r eval=FALSE} halo_pipeline.R -m my_project_manifest.txt

OR
```{r eval=FALSE}
counts.R -m counts_manifest.txt

then {r eval=FALSE} pie_charts.R -m pie_charts_manifest.txt



bic-mskcc/halo documentation built on Jan. 27, 2018, 12:19 a.m.