Helpful_links.Rmd

## Papers
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There is no shortage of papers to read regarding different methods used for CyTOF. Some that I found useful are:

1. <a href="http://www.nature.com/ni/journal/v17/n8/abs/ni.3485.html">Newell EW	& Cheng Y. Mass cytometry: blessed with the curse of dimensionality. (2016) Nature Immunology 17, 890–895 </a>

2. <a href="http://www.nature.com/nri/journal/v16/n7/full/nri.2016.56.html">Saeys Y,	Gassen SV	& Lambrecht BN. Computational flow cytometry: helping to make sense of high-dimensional immunology data. (2016) Nature Reviews Immunology 16, 449–462</a>

3. <a href="http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22271/abstract"> R. Finck et al., Normalization of mass cytometry data with bead standards. (2013) Cytometry Part A. 83A, 483–494.

4. <a href="https://www.nature.com/nprot/journal/v10/n2/full/nprot.2015.020.html"> R. Zunder et al., Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. (2015) Nat. Protocols. 10, 316–333 </a>

5. <a href="https://f1000research.com/articles/6-748/v1"> Nowicka M. et al. CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets </a>

6. <a href="https://www.nature.com/articles/nmeth.4295">Lun et al., Testing for differential abundance in mass cytometry data.Nature Methods volume 14, pages 707–709 (2017)</a>

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## Web Resources

1. <a href="http://flowrepository.org/"> Flowrepository </a>
2. <a href="https://community.cytobank.org/"> Cytobank Community </a>
3. <a href="http://cytoforum.stanford.edu/">  Cytoforum </a>

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## R Packages
Following are  some of the best packages available for CyTOF analysis

1. <a href="https://bioconductor.org/packages/release/bioc/html/CATALYST.html"> CATALYST </a>
2. <a  href="http://bioconductor.org/packages/release/bioc/html/flowCore.html"> FlowCore </a>
3. <a href="http://bioconductor.org/packages/release/bioc/html/cytofkit.html"> Cytofkit </a>