bioinformatics-core-shared-training
diff --git a/‎GeneticPracticalPackageInstall.R‎
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diff --git a/‎Lectures/Lect1_HTSeq_Introduction_Sept2014.pdf‎
16.4 MB b/‎Lectures/Lect1_HTSeq_Introduction_Sept2014.pdf‎
16.4 MB
diff --git a/‎Lectures/Lect2-StringsAndRanges.pdf‎
772 KB b/‎Lectures/Lect2-StringsAndRanges.pdf‎
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diff --git a/‎Lectures/Lect3-CopyNumber_HT.pdf‎
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diff --git a/‎Lectures/Lect4-DesignStatistics_HTSeq.pdf‎
4.48 MB b/‎Lectures/Lect4-DesignStatistics_HTSeq.pdf‎
4.48 MB
diff --git a/‎Lectures/Lect5_RNAseq_Sept2014.pdf‎
8.71 MB b/‎Lectures/Lect5_RNAseq_Sept2014.pdf‎
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diff --git a/‎Lectures/Lect6a_Introduction_to_Annotation.pdf‎
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diff --git a/‎Lectures/Lect6b_GenomeAnnotation.pdf‎
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diff --git a/‎Lectures/Lect7a_ChIP-Seq_Data_Analysis.pdf‎
4.16 MB b/‎Lectures/Lect7a_ChIP-Seq_Data_Analysis.pdf‎
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diff --git a/‎Lectures/Lect7b_ChIP-Seq Data Analysis.pdf‎
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+source("http://www.bioconductor.org/biocLite.R")
+options(BioC_mirror = c("Cambridge" = "http://mirrors.ebi.ac.uk/bioconductor/"))
+options(repos = c("CRAN" = "http://cran.ma.imperial.ac.uk"))
+biocLite(c("Biostrings", "ShortRead", "DESeq", "edgeR","biomaRt", "BSgenome",
+        "BSgenome.Dmelanogaster.UCSC.dm3", "org.Dm.eg.db",
+        "TxDb.Dmelanogaster.UCSC.dm3.ensGene", "pasillaBamSubset", "pasilla",
+        "rtracklayer", "ggbio", "vsn","gplots","RColorBrewer","chipseq","htSeqTools","limma","NBPSeq","tweeDEseqCountData","org.Hs.eg.db","Rcade", "exomeCopy","CNAnorm", "ChIPQC","TxDb.Hsapiens.UCSC.hg19.knownGene","BSgenome.Hsapiens.UCSC.hg19"))
+
+##Also need to install spp_1.11.tar.gz which requires the 'boost' library.
+
+