├── Flowchart_V2.1.png ├── LICENSE ├── READMe.md ├── Rscripts ├── DE_deseq_genes_bedtools.R ├── DE_deseq_genes_htseq.R └── DE_dexseq_exon.R ├── download_RNASeq_reads_and_QC.sh ├── download_genome_and_annotation.sh ├── download_install_tools.sh ├── metadata.txt ├── project_config.sh ├── quantification.sh └── reference_based_alignment.sh /Flowchart_V2.1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/Flowchart_V2.1.png -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/LICENSE -------------------------------------------------------------------------------- /READMe.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/READMe.md -------------------------------------------------------------------------------- /Rscripts/DE_deseq_genes_bedtools.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/Rscripts/DE_deseq_genes_bedtools.R -------------------------------------------------------------------------------- /Rscripts/DE_deseq_genes_htseq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/Rscripts/DE_deseq_genes_htseq.R -------------------------------------------------------------------------------- /Rscripts/DE_dexseq_exon.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/Rscripts/DE_dexseq_exon.R -------------------------------------------------------------------------------- /download_RNASeq_reads_and_QC.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/download_RNASeq_reads_and_QC.sh -------------------------------------------------------------------------------- /download_genome_and_annotation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/download_genome_and_annotation.sh -------------------------------------------------------------------------------- /download_install_tools.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/download_install_tools.sh -------------------------------------------------------------------------------- /metadata.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/metadata.txt -------------------------------------------------------------------------------- /project_config.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/project_config.sh -------------------------------------------------------------------------------- /quantification.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/quantification.sh -------------------------------------------------------------------------------- /reference_based_alignment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grimmlab/BookChapter-RNA-Seq-Analyses/HEAD/reference_based_alignment.sh --------------------------------------------------------------------------------