├── .gitignore ├── .gitmodules ├── CONDUCT.md ├── Course_Materials ├── 02_Preprocessing_Data.Rmd ├── 03_Linear_Models.Rmd ├── 04_DE_analysis_with_DESeq2.Rmd ├── 05_Annotation_and_Visualisation.Rmd ├── 06_Gene_set_testing.Rmd ├── B_FastQC_practical.Rmd ├── C_Alignment_with_HISAT2_practical.Rmd ├── D_QC_of_aligned_reads_practical.Rmd ├── E_Read_Counts_with_Subread.Rmd ├── Robjects │ ├── Annotated_Results_LvV.RData │ ├── DE.RData │ ├── Ensembl_annotations.RData │ ├── Full_annotation.RData │ ├── first1000annotation.rds │ ├── mouse_H_v5.RData │ ├── mouse_c2_v5.RData │ └── preprocessing.RData ├── data │ ├── GSE60450_Lactation.featureCounts │ ├── GSE60450_Lactation.featureCounts.summary │ ├── SampleInfo.Corrected.txt │ ├── SampleInfo.txt │ └── VirginVsLactating_Results_Annotated.txt ├── metrics │ ├── MCL1.DG.alignment_metrics.txt │ ├── MCL1.DG.mkdup.bam.metrics.txt │ ├── MCL1.DG.rna_metrics.txt │ ├── MCL1.DH.alignment_metrics.txt │ ├── MCL1.DH.mkdup.bam.metrics.txt │ ├── MCL1.DH.rna_metrics.txt │ ├── MCL1.DI.alignment_metrics.txt │ ├── MCL1.DI.mkdup.bam.metrics.txt │ ├── MCL1.DI.rna_metrics.txt │ ├── MCL1.DJ.alignment_metrics.txt │ ├── MCL1.DJ.mkdup.bam.metrics.txt │ ├── MCL1.DJ.rna_metrics.txt │ ├── MCL1.DK.alignment_metrics.txt │ ├── MCL1.DK.mkdup.bam.metrics.txt │ ├── MCL1.DK.rna_metrics.txt │ ├── MCL1.DL.alignment_metrics.txt │ ├── MCL1.DL.mkdup.bam.metrics.txt │ ├── MCL1.DL.rna_metrics.txt │ ├── MCL1.DM.alignment_metrics.txt │ ├── MCL1.DM.mkdup.bam.metrics.txt │ ├── MCL1.DM.rna_metrics.txt │ ├── MCL1.LA.alignment_metrics.txt │ ├── MCL1.LA.mkdup.bam.metrics.txt │ ├── MCL1.LA.rna_metrics.txt │ ├── MCL1.LB.alignment_metrics.txt │ ├── MCL1.LB.mkdup.bam.metrics.txt │ ├── MCL1.LB.rna_metrics.txt │ ├── MCL1.LC.alignment_metrics.txt │ ├── MCL1.LC.mkdup.bam.metrics.txt │ ├── MCL1.LC.rna_metrics.txt │ ├── MCL1.LD.alignment_metrics.txt │ ├── MCL1.LD.mkdup.bam.metrics.txt │ ├── MCL1.LD.rna_metrics.txt │ ├── MCL1.LE.alignment_metrics.txt │ ├── MCL1.LE.mkdup.bam.metrics.txt │ ├── MCL1.LE.rna_metrics.txt │ ├── MCL1.LF.alignment_metrics.txt │ ├── MCL1.LF.mkdup.bam.metrics.txt │ ├── MCL1.LF.rna_metrics.txt │ ├── MCL1.LG.alignment_metrics.txt │ ├── MCL1.LG.mkdup.bam.metrics.txt │ ├── MCL1.LG.rna_metrics.txt │ ├── multiqc_data │ │ ├── multiqc.log │ │ ├── multiqc_data.json │ │ ├── multiqc_general_stats.txt │ │ ├── multiqc_picard_AlignmentSummaryMetrics.txt │ │ ├── multiqc_picard_RnaSeqMetrics.txt │ │ ├── multiqc_picard_dups.txt │ │ └── multiqc_sources.txt │ └── multiqc_report.html ├── ref.bib ├── small_bams │ ├── MCL1.DG.15.sm.bam │ ├── MCL1.DG.15.sm.bam.bai │ ├── MCL1.DH.15.sm.bam │ ├── MCL1.DH.15.sm.bam.bai │ ├── MCL1.DI.15.sm.bam │ ├── MCL1.DI.15.sm.bam.bai │ ├── MCL1.DJ.15.sm.bam │ ├── MCL1.DJ.15.sm.bam.bai │ ├── MCL1.DK.15.sm.bam │ ├── MCL1.DK.15.sm.bam.bai │ ├── MCL1.DL.15.sm.bam │ ├── MCL1.DL.15.sm.bam.bai │ ├── MCL1.LA.15.sm.bam │ ├── MCL1.LA.15.sm.bam.bai │ ├── MCL1.LB.15.sm.bam │ ├── MCL1.LB.15.sm.bam.bai │ ├── MCL1.LC.15.sm.bam │ ├── MCL1.LC.15.sm.bam.bai │ ├── MCL1.LD.15.sm.bam │ ├── MCL1.LD.15.sm.bam.bai │ ├── MCL1.LE.15.sm.bam │ ├── MCL1.LE.15.sm.bam.bai │ ├── MCL1.LF.15.sm.bam │ ├── MCL1.LF.15.sm.bam.bai │ └── Mus_musculus.GRCm38.97.chr15.gtf └── solutions │ ├── 02_Preprocessing_Data.Solutions.Rmd │ ├── 04_DE_analysis.Solutions.Rmd │ ├── 05_Annotation_and_Visualisation.Solutions.Rmd │ ├── 06_Gene_set_testing.Solutions.Rmd │ ├── C_Alignment_with_HISAT2.Solutions.Rmd │ ├── D_QC_of_aligned_reads.Solutions.Rmd │ └── E_Read_Counts_with_Subread.Solutions.Rmd ├── Dockerfile ├── LICENSE.html ├── LICENSE.md ├── New_Day_1_Outline.md ├── README.md ├── Supplementary_Materials ├── R_Code_reference.Rmd ├── S1_Getting_raw_reads_from_SRA.Rmd ├── S1_Getting_raw_reads_from_SRA.html ├── S2_Read_Counts_with_Subread.Rmd ├── S2_Read_Counts_with_Subread.html ├── S3_Annotation_and_Visualisation.Rmd ├── S3_Annotation_and_Visualisation.nb.html ├── install_bioc_packages.R └── ref.bib ├── _config.yml ├── additional_scripts ├── 01_Introduction_to_RNAseq_Analysis_in_R.Rmd ├── A_Introduction_to_RNAseq_Methods.Rmd ├── B_FastQC.Rmd ├── C_Alignment_with_HISAT2.Rmd ├── D_QC_of_aligned_reads.Rmd ├── Day1.Rmd ├── LinuxCheatSheet.Rmd ├── LinuxCheatSheet.pdf ├── MCL1.DL.RNA_metrics.txt ├── MCL1.LG.RNA_metrics.txt ├── MakeBatchEffectPlot.R ├── Making_the_annotation_table.R ├── QC_aligned_reads_plots.R ├── download_align_count │ ├── SRA_ids.txt │ ├── targets2.txt │ ├── xAlign.sh │ ├── xExtractFQ.sh │ ├── xFeatureCounts.sh │ └── xPreFetchSRA.sh ├── images └── stylesheet.css ├── css ├── book.css ├── bootstrap │ ├── bootstrap-js │ │ └── bootstrap.js │ ├── bootstrap-theme.css │ ├── bootstrap-theme.css.map │ ├── bootstrap.css │ ├── bootstrap.css.map │ └── fonts │ │ ├── glyphicons-halflings-regular.eot │ │ ├── glyphicons-halflings-regular.svg │ │ ├── glyphicons-halflings-regular.ttf │ │ ├── glyphicons-halflings-regular.woff │ │ └── glyphicons-halflings-regular.woff2 ├── stylesheet.css ├── swc-print.css └── swc.css ├── docker └── Dockerfile ├── history.md ├── html ├── 01_Introduction_to_RNAseq_Analysis_in_R.html ├── 02_Preprocessing_Data.Solutions.html ├── 02_Preprocessing_Data.html ├── 03_Linear_Models.nb.html ├── 04_DE_analysis.Solutions.html ├── 04_DE_analysis.Solutions.nb.html ├── 04_DE_analysis_with_DESeq2.html ├── 05_Annotation_and_Visualisation.Solutions.html ├── 05_Annotation_and_Visualisation.html ├── 06_Gene_set_testing.Solutions.html ├── 06_Gene_set_testing.html ├── A_Introduction_to_RNAseq_Methods.html ├── B_FastQC.html ├── B_FastQC_practical.html ├── C_Alignment_with_HISAT2.Solutions.html ├── C_Alignment_with_HISAT2.html ├── C_Alignment_with_HISAT2_Practical.html ├── D_QC_of_aligned_reads.Solutions.html ├── D_QC_of_aligned_reads.html ├── D_QC_of_aligned_reads_practical.html ├── E_Read_Counts_with_Subread.Solutions.html ├── E_Read_Counts_with_Subread.html └── images ├── images ├── BatchEffect.svg ├── BatchEffecta.svg ├── BatchEffectb.svg ├── BioRep.jpg ├── CRUK_Cambridge_Institute.png ├── CRUK_Cambridge_Major Centre logo.jpg ├── Counting.png ├── Coverage.png ├── DepthvReps.jpg ├── DifferenceInMeans.png ├── EMBJ-34-2727-g003.jpg ├── Experimental_Design-C_Ambrosino.jpg ├── FastQC_logo.png ├── GOenrichment.svg ├── GSEA-homegraphic.gif ├── GappedAlignment.svg ├── GenomicLocations.svg ├── GeometricScaling.svg ├── Hamy2016PlosOneHC.png ├── Hamy2016PlosOneNetworkTrp.png ├── Heatmap.svg ├── IlluminaLibraryPrep.png ├── IlluminaLibraryPrep1.png ├── IlluminaLibraryPrep2.png ├── LinearityOfCounts.png ├── MSigDBTrsp.png ├── NegativeBinomialDistribution.png ├── Noise.svg ├── OtherRNA.svg ├── PlateBad.svg ├── PlateEmpty.svg ├── PlateGood.svg ├── RNA_Extraction.svg ├── RNAseq_WorkFlow.png ├── SAM_alignment_1.png ├── SAM_alignment_1b.png ├── SAM_alignment_1c.png ├── SAM_alignment_2.png ├── SAM_alignment_3.png ├── SAM_header_1.png ├── SAM_header_2.png ├── SAMflags.png ├── SRAlignment.svg ├── SamplingBias.svg ├── SequencingArtefacts.png ├── TechRep.jpg ├── TranscriptCoverage.svg ├── TranscriptLength.svg ├── Volcano.png ├── attendance.gif ├── bad3.png ├── combine_banner.png ├── combine_banner_small.png ├── dispersion.png ├── fq.png ├── fq_headers.png ├── fq_quality.png ├── fq_seq.png ├── good1.png ├── good3.png ├── mRNA.svg ├── mmu03320.pathview.png ├── mmu04060.pathview.png ├── multiplexing.jpg ├── polyA_selection.png ├── polyA_selection.svg ├── rRNA.svg ├── ribominus_selection.png ├── ribominus_selection.svg ├── scaling.svg ├── splicing.svg ├── um2.png ├── workflow.svg └── workflow_3Day.svg ├── index.md ├── install_packages.R ├── instructor_materials ├── .Rhistory ├── 01_Read_Counts_with_Subread_IM.Rmd ├── 02_Preprocessing_Data_IM.Rmd ├── 04_DE_analysis_with_DESeq2_IM.Rmd ├── 05_Annotation_and_Visualisation_IM.Rmd └── 06_Gene_set_testing_IM.Rmd └── slides ├── Introduction_to_RNAseq_Methods.html └── LinearModels.pdf /.gitignore: -------------------------------------------------------------------------------- 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