Bookdown report of SRP199678
Generated on 2022-04-04
Introduction
As an essential part of the RNASequest framework, the Expression Analysis (EA) pipeline analyzes RNAseq data provided by the user, or from the NCBI/GEO database, and generates results for interactive visualization.
This is a summary report generated by EAreport (part of Expression Analysis) using Bookdown.
This report contains basic plots and tables generated by the pipeline.
Project overview
Here is a brief overview of the project:
Project Name: SRP199678
Species: human
Description: Cx3cr1- deficient microglia exhibit a premature aging transcriptome
Number of Samples: 155
Number of Groups: 36
Number of Genes/Proteins: 40893
Number of Comparisons: 3
Number of Samples in Each Group:
| grp14 | grp8 | grp11 | grp17 | grp7 | grp12 | grp1 | grp25 | grp4 | grp5 | grp6 | grp3 | grp32 | grp23 | grp22 | grp2 | grp24 | grp33 | grp34 | grp27 | grp19 | grp13 | grp10 | grp26 | grp18 | grp28 | grp35 | grp36 | grp30 | grp21 | grp16 | grp15 | grp29 | grp20 | grp31 | grp9 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| count | 5 | 6 | 5 | 4 | 6 | 5 | 7 | 3 | 6 | 6 | 6 | 7 | 3 | 4 | 4 | 7 | 4 | 2 | 2 | 3 | 4 | 5 | 5 | 3 | 4 | 3 | 2 | 2 | 3 | 4 | 5 | 5 | 3 | 4 | 3 | 5 |
Project files
The EA pipeline also produced several files under the working directory:
notAdjusted_Covariate_PC_Results.rds
notAdjusted_Covariate_PC_Results.xlsx
notAdjusted_PCA_Plots.pdf
notAdjusted_Significant_Categorical_Covariates.pdf
notAdjusted_Significant_Numeric_Covariates.pdf
sequenceQC.pdf
sequenceQC.unionTop.TPM.csv
For more flexible and interactive visualization, please upload the following Rdata files to Quickomics.
SRP199678_estCount.rds
SRP199678_network.RData
SRP199678.RData
SRP199678.csv
The following sections are included in this bookdown report: