Commit d4c4f74d authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Update README.md

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* PI: Douglas W. Strand, PhD
* <a href="https://orcid.org/0000-0002-0746-927X" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon">orcid.org/0000-0002-0746-927X</a>
* PI Email: [douglas.strand@utsouthwestern.edu](mailto:douglas.strand@utsouthwestern.edu)
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* **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")**
* **Publication at:**
* Cell Reports: PENDING
* [BioRxiv](https://www.biorxiv.org/content/early/2018/10/15/439935)
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Data Analysis
-------------
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* dplyr (v0.7.6)
* viridis (v0.5.1)
* *and all dependencies*
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* **HOW TO RUN**
* 1 Run on 3 patient aggregate
* run bash script [sc\_TissueMapper\-Pr.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-Pd.sh)
* 2 Run on 1st patent FACS samples
* run bash script [sc\_TissueMapper\-D17\_FACS.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-D17_FACS.sh)
* 3 Run on 2nd patient FACS samples
* run bash script [sc\_TissueMapper\-D27\_FACS.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-D27_FACS.sh)
* 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)
* 5 Aggregate and compare several downsamples from # 4
* 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)
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* **Pipeline:**
* Link cellranger count/aggr output to analysis
* Create demultiplex file to add custom sample groups
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