Hi community members ! I would be very happy to recieve advices from you. I have scRNA-Seq data and would like to start with the analysis part. I already went through QC and alignment process but I would be needing a good comprehensive analysis protocol for post alignment procedures and statistical analysis. Your suggesntions will be appriciated.
#RNAseq #RNA-Seq #scRNA-Seq #Genomics #Bioinformatics #Computational_Biology
Check this workflow from Bioconductor (https://bioconductor.org/packages/release/workflows/html/simpleSingleCell.html).
Here are two indispensable resources to get started:
https://github.com/hemberg-lab/scRNA.seq.course
https://github.com/seandavi/awesome-single-cell
Hi, I would also suggest to have a look at Scater package.
https://bioconductor.org/packages/release/bioc/html/scater.html
https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette-dataviz.html
https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette-intro.html
and MAST package for differential expression analysis.
https://bioconductor.org/packages/release/bioc/html/MAST.html
Best,
Michail
This is the same as the first one of Christopher Benway's suggested links, but it goes straight to the tutorial, in case you don´t know where to start: https://hemberg-lab.github.io/scRNA.seq.course/
The SCDE package is a good one to start with for pathway analysis:
http://hms-dbmi.github.io/scde/pagoda.html
http://hms-dbmi.github.io/scde/tutorials.html
They have very handy tutorials with curated data as well that you can try and replicate to get a general understanding of the package before moving on to your own datasets.
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