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STAT540-UBC · Feb 13, 2024 · 9d87990 · 9d87990
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diff --git a/lect10-RNAseq/README.md b/lect10-RNAseq/README.md
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+# Lecture 10 Pre-reading:
+
+* Sections 1-3 in Chapter 1 (Generative Models for Discrete Data) in ["Modern Statistics for Modern Biology"](http://web.stanford.edu/class/bios221/book/) by Susan Holmes and Wolfgang Huber:
+
+  * [1.1: Overview & goals](https://www.huber.embl.de/msmb/01-chap.html)
+  * [1.2: A real example](https://www.huber.embl.de/msmb/01-chap.html#a-real-example)
+  * [1.3: Using discrete probability models](https://www.huber.embl.de/msmb/01-chap.html#using-discrete-probability-models)
+
+* Chapter 8 (High-Throughput Count data) in in ["Modern Statistics for Modern Biology"](http://web.stanford.edu/class/bios221/book/) by Susan Holmes and Wolfgang Huber:
+
+  * [8.1: High-Throughput Count Data](https://www.huber.embl.de/msmb/01-chap.html)
+
+  * [8.4: Modeling count data](https://www.huber.embl.de/msmb/08-chap.html#modeling-count-data)
+
+* [This deep dive comparative analysis of RNA-seq data with several different approaches](https://github.com/STAT540-UBC/resources/blob/main/rnaseqdiffex-examples/examples-RNAseq.md)
+
diff --git a/lect10-RNAseq/data/Gompers_NN_CountMatrix.txt b/lect10-RNAseq/data/Gompers_NN_CountMatrix.txt
diff --git a/lect10-RNAseq/data/nn.4592-S4.fixed.csv b/lect10-RNAseq/data/nn.4592-S4.fixed.csv
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+Number,Sample.ID,Stage (DPC),Sex (1=male),Group (1=WT),SeqRun,Mapped Reads,Feature Counts
+1,Sample_ANAN001A,12.5,2,2,A,42452222,37655856
+2,Sample_ANAN001B,12.5,1,1,A,54503162,47106938
+3,Sample_ANAN001C,12.5,1,1,A,44978512,40448118
+4,Sample_ANAN001D,12.5,2,2,A,50099336,44993589
+5,Sample_ANAN001E,12.5,2,2,A,47163546,41840678
+6,Sample_ANAN001F,12.5,2,1,A,43893480,39483622
+7,Sample_ANAN001G,12.5,2,2,A,53208684,47697298
+8,Sample_ANAN001H,12.5,2,1,A,38925414,35056860
+9,Chd8.e14.S12,14.5,1,1,B,23622816,19586363
+10,Chd8.e14.S13,14.5,2,1,B,23974703,21019829
+11,Chd8.e14.S14,14.5,1,2,B,20624874,17550908
+12,Chd8.e14.S16,14.5,2,2,B,23678463,20868107
+13,Chd8.e14.S17,14.5,2,1,B,24586763,21687086
+14,Chd8.e14.S18,14.5,2,2,B,21340900,18777139
+15,Chd8.e14.S19,14.5,2,2,B,18122632,16070057
+16,Chd8.e14.S20,14.5,1,2,B,13101999,11564438
+17,Chd8.e14.S21,14.5,1,2,B,24789597,21965092
+18,Chd8.e17.5.1_S158,17.5,1,2,C,26386249,22250739
+19,Chd8.e17.5.2_S159,17.5,1,1,C,17370801,13248769
+20,Chd8.e17.5.4_S161,17.5,2,1,C,26373431,21792781
+21,Chd8.e17.5.5_S162,17.5,1,2,C,24624012,20225460
+22,Chd8.e17.5.6_S163,17.5,1,2,C,24067586,20631352
+23,Chd8.e17.5.1_S1,17.5,2,2,D,53271915,44725224
+24,Chd8.e17.5.2_S2,17.5,1,2,D,42120091,36001004
+25,Chd8.e17.5.3_S3,17.5,2,2,D,35016567,29824599
+26,Chd8.e17.5.4_S4,17.5,2,1,D,41214297,33892057
+27,Chd8.e17.5.5_S5,17.5,2,2,D,45448630,38148553
+28,Chd8.P0.S1,21,2,2,E,26285226,21585939
+29,Chd8.P0.S10,21,2,1,E,19181637,15990423
+30,Chd8.P0.S11,21,2,1,E,24998878,20762484
+31,Chd8.P0.S2,21,2,2,E,21838632,18621877
+32,Chd8.P0.S3,21,2,2,E,22452065,18860113
+33,Chd8.P0.S4,21,2,2,E,23383616,19820642
+34,Chd8.P0.S5,21,2,1,E,25083466,21084415
+35,Chd8.P0.S6,21,1,2,E,22404548,18694448
+36,Chd8.P0.S7,21,1,2,E,23407157,19750493
+37,Chd8.P0.S8,21,2,1,E,27374372,22956532
+38,Chd8.P0.S9,21,2,1,E,19254462,15964473
+39,Chd8.adult.S23,77,1,1,H,60579458,43534157
+40,Chd8.adult.S24,77,1,2,H,37739455,27917136
+41,Chd8.adult.S25,77,1,2,H,38258328,28336157
+42,Chd8.adult.S28,77,1,2,H,34485611,24349366
+43,Chd8.adult.S29,77,1,1,H,38676767,27849589
+44,Chd8.adult.S31,77,2,1,H,33572184,23569556
diff --git a/lect10-RNAseq/img/DESeq2.png b/lect10-RNAseq/img/DESeq2.png
diff --git a/lect10-RNAseq/img/GompersDesign.png b/lect10-RNAseq/img/GompersDesign.png
diff --git a/lect10-RNAseq/img/GompersHeatmap.png b/lect10-RNAseq/img/GompersHeatmap.png
diff --git a/lect10-RNAseq/img/SequenceSpace.pdf b/lect10-RNAseq/img/SequenceSpace.pdf
diff --git a/lect10-RNAseq/img/arraytransf.png b/lect10-RNAseq/img/arraytransf.png
diff --git a/lect10-RNAseq/img/clusterdensity.png b/lect10-RNAseq/img/clusterdensity.png
diff --git a/lect10-RNAseq/img/comparisons.png b/lect10-RNAseq/img/comparisons.png
diff --git a/lect10-RNAseq/img/dispersion.png b/lect10-RNAseq/img/dispersion.png
diff --git a/lect10-RNAseq/img/edgeR.png b/lect10-RNAseq/img/edgeR.png
diff --git a/lect10-RNAseq/img/genelength.png b/lect10-RNAseq/img/genelength.png
diff --git a/lect10-RNAseq/img/mean_variance.png b/lect10-RNAseq/img/mean_variance.png
diff --git a/lect10-RNAseq/img/mean_variance_voom.png b/lect10-RNAseq/img/mean_variance_voom.png
diff --git a/lect10-RNAseq/img/mvvplots.png b/lect10-RNAseq/img/mvvplots.png
diff --git a/lect10-RNAseq/img/overdisp.png b/lect10-RNAseq/img/overdisp.png
diff --git a/lect10-RNAseq/img/quantilenorm.png b/lect10-RNAseq/img/quantilenorm.png
diff --git a/lect10-RNAseq/img/rpkm.png b/lect10-RNAseq/img/rpkm.png
diff --git a/lect10-RNAseq/img/seqRecap.png b/lect10-RNAseq/img/seqRecap.png
diff --git a/lect10-RNAseq/img/seqdepth.png b/lect10-RNAseq/img/seqdepth.png
diff --git a/lect10-RNAseq/img/seqspace.png b/lect10-RNAseq/img/seqspace.png
diff --git a/lect10-RNAseq/img/summarizedexperiment.png b/lect10-RNAseq/img/summarizedexperiment.png
diff --git a/lect10-RNAseq/lect10-RNAseq-beamer.pdf b/lect10-RNAseq/lect10-RNAseq-beamer.pdf