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README.md
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@@ -12,7 +12,9 @@ Determining cellular heterogeneity in the human prostate with single-cell RNA se
@@ -12,7 +12,9 @@ Determining cellular heterogeneity in the human prostate with single-cell RNA se
* PI Email: [douglas.strand@utsouthwestern.edu](mailto:douglas.strand@utsouthwestern.edu)
* PI Email: [douglas.strand@utsouthwestern.edu](mailto:douglas.strand@utsouthwestern.edu)
* **ANALYZED DATA FOR QUERYING AT: [StrandLab.net](http://strandlab.net/analysis.php)**
* **ANALYZED DATA FOR QUERYING AT: [StrandLab.net](http://strandlab.net/analysis.php)**
* **Raw data at: [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120716) & [GenitoUrinary Development Molecular Anatomy Project (GUDMAP)]("https://doi.org/10.25548/W-R8CM")**
* **Raw data at: [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120716) & [GenitoUrinary Development Molecular Anatomy Project (GUDMAP)]("https://doi.org/10.25548/W-R8CM")**
* **Publication at: [BioRxiv](https://www.biorxiv.org/content/early/2018/10/15/439935)**
* **Publication at:**
 
* Cell Reports: PENDING
 
* [BioRxiv](https://www.biorxiv.org/content/early/2018/10/15/439935)
Data Analysis
Data Analysis
-------------
-------------
@@ -53,7 +55,7 @@ Data Analysis
@@ -53,7 +55,7 @@ Data Analysis
* 4 Run on several downsamples from 1 sample from 1st patient
* 4 Run on several downsamples from 1 sample from 1st patient
* run bash script [sc\_TissueMapper\-DS\_D17.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-DS_D17.sh)
* run bash script [sc\_TissueMapper\-DS\_D17.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-DS_D17.sh)
* 5 Aggregate and compare several downsamples from #4
* 5 Aggregate and compare several downsamples from #4
* run bash script [sc\_TissueMapper\_RUN.DS\_D17.aggr.R](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/r.scripts/sc_TissueMapper_RUN.DS_D17.aggr.R)
* run r script [sc\_TissueMapper\_RUN.DS\_D17.aggr.R](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/r.scripts/sc_TissueMapper_RUN.DS_D17.aggr.R)
* **Pipeline:**
* **Pipeline:**
* Link cellranger count/aggr output to analysis
* Link cellranger count/aggr output to analysis
* Create demultiplex file to add custom sample groups
* Create demultiplex file to add custom sample groups
@@ -88,8 +90,6 @@ Data Analysis
@@ -88,8 +90,6 @@ Data Analysis
* Lineage:
* Lineage:
* "DEG\_Epi_5FC.txt" DWS generated DEGs of epithelia from FACS population (bulk) RNA-sequencing
* "DEG\_Epi_5FC.txt" DWS generated DEGs of epithelia from FACS population (bulk) RNA-sequencing
* "DEG\_FMSt_5FC.txt" DWS generated DEGs of fibromuscular stroma from FACS population (bulk) RNA-sequencing
* "DEG\_FMSt_5FC.txt" DWS generated DEGs of fibromuscular stroma from FACS population (bulk) RNA-sequencing
* "genes.deg.Epi.csv" DWS generated DEGs of epithelial cells from scRNA-Seq of 3 patient aggregate
* "genes.deg.St.csv" DWS generated DEGs of stromal cells from scRNA-Seq of 3 patient aggregate
* Epithelia:
* Epithelia:
* "DEG\_BE_5FC.txt" DWS generated DEGs of basal epithelia from FACS population (bulk) RNA-sequencing
* "DEG\_BE_5FC.txt" DWS generated DEGs of basal epithelia from FACS population (bulk) RNA-sequencing
* "DEG\_LE_5FC.txt" DWS generated DEGs of luminal epithelia from FACS population (bulk) RNA-sequencing
* "DEG\_LE_5FC.txt" DWS generated DEGs of luminal epithelia from FACS population (bulk) RNA-sequencing