GitHub - TimBlokker/RNA_Sequencing: In total there are 3 jupyter notebooks together with 3 html files for ease of access in this repository. (1) Master notebook & FastQC and Mapping of reads using star and subsequent feature count (this notebook), (2) the DESeq2 analysis in R for the statistical analysis, (3) Functional analysis using arbitrary (GProfiler, iRegulon) and "leading edge" (Gorilla, GSEA) cut-offs. The dataset was taken from here: https://www.ncbi.nlm.nih.gov/sra/SRX8335650 and is accompanying the publication by Carmona-Rivera et al. 2020 https://insight.jci.org/articles/view/139388.

TimBlokker / RNA_Sequencing Public

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In total there are 3 jupyter notebooks together with 3 html files for ease of access in this repository. (1) Master notebook & FastQC and Mapping of reads using star and subsequent feature count (this notebook), (2) the DESeq2 analysis in R for the statistical analysis, (3) Functional analysis using arbitrary (GProfiler, iRegulon) and "leading e…

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Name		Name	Last commit message	Last commit date
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.ipynb_checkpoints		.ipynb_checkpoints
DeSeq2.html		DeSeq2.html
DeSeq2.ipynb		DeSeq2.ipynb
Functional_Analysis.html		Functional_Analysis.html
Functional_Analysis.ipynb		Functional_Analysis.ipynb
Master_RNAseq.map.count.html		Master_RNAseq.map.count.html
Master_RNAseq.map.count.ipynb		Master_RNAseq.map.count.ipynb