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scrnaseq-bulkrnaseq's Introduction

Single-cell and bulk RNASeq analysis

Example analysis scripts with Seurat, Monocle, and other R packages for normalization, scaling, dimensionality reduction techniques (tSNE, PCA), differential gene expression, and visualization. For scRNASeq from 10X Genomics Chromium platform, I use cellranger demultiplexing, and for the ddSeq platform, I use Illumina BaseSpace automated demultiplexing. Both these programs then run a customized STAR alignment. Seurat is my package of choice for single-cell data. For bulk RNASeq, I use a manual STAR-htseq-DESeq2 pipeline but may switch to limma instead of DESeq2. For visualization purposes, I use the R packages' built-in functions or use custom ggplot2 and occasionally base R graphics functions.

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scrnaseq-bulkrnaseq's Issues

Can you provide your example document？

Thank you for your perfect example in using moncle.
I am a student who is going to perform pseudo-time analysis on single-cell data by moncle. I am confused that the database can only be downloaded to the expression matrix, phenoData and featureData files need to be created and written by ourselves?
I will appreciate it if you can provide your documentation (Aggregation6.csv) for my reference.

Could you please show me how to convert a Seurat object as the input of FateID

Dear cemalley,
Thank you for your nice example of using FateID.
I am a beginner in the siRNA-seq analysis.
I have done the clustering and the identification of cell-types in my scRNA-seq datasets using Seurat v3.
I plan to use FateID to do the downstream analysis, but I have no idea how to convert the Seurat object into the data format that could be used in FateID.
Could you please teach me how to do the data format conversion from Seurat object, since I noticed that you are also using Seurat package.

Thank you in advance.

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