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index.Rmd
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index.Rmd
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---
title: "Home"
site: workflowr::wflow_site
output:
workflowr::wflow_html:
toc: true
---
I refer to [my blog](https://davetang.org/muse/) often to look up notes and code I have written. I will recreate my blog posts here, to make it easier to reuse and maintain my code. Some posts only exist here and not on my blog, so there is no `original` hyperlink back to my blog.
## Blog posts
### Visualisation
* Making a heatmap in R with the pheatmap package - [original](https://davetang.org/muse/2018/05/15/making-a-heatmap-in-r-with-the-pheatmap-package/) / [updated](pheatmap.html)
* Visualising Google Trends results with R - [original](https://davetang.org/muse/2018/12/31/visualising-google-trends-results-with-r/) / [updated](google_trends.html)
* Complex UpSet plots - original / [updated](complex_upset.html)
* Gene expression heatmap using ARCHS4 data - original / [updated](gene_heatmap.html)
* Network graph using R Plotly - original / [updated](plotly_network.html)
* Making a heatmap in R with the ComplexHeatmap package - original / [updated](complex_heatmap.html)
### Bioinformatics
* Read GTF file into R - [original](https://davetang.org/muse/2017/08/04/read-gtf-file-r/) / [updated](read_gtf.html)
* Gene Ontology Enrichment Analysis - [original](https://davetang.org/muse/2010/11/10/gene-ontology-enrichment-analysis/) / [updated](go_enrichment.html)
* Using the R `seqinr` package - [original](https://davetang.org/muse/2013/05/09/using-the-r-seqinr-package/) / [updated](seqinr.html)
* Using the Bioconductor ensembldb package - original / [updated](ensembldb.html)
* Using the fast preranked gene set enrichment analysis (fgsea) package - [original](https://davetang.org/muse/2018/01/10/using-fast-preranked-gene-set-enrichment-analysis-fgsea-package/) / [updated](fgsea.html)
* Using the Bioconductor GenomicRanges package - [original](https://davetang.org/muse/2013/01/02/iranges-and-genomicranges/) / [updated](genomic_ranges.html)
* Position weight matrix - [original](https://davetang.org/muse/2013/10/01/position-weight-matrix/) / [updated](pwm.html)
* Tissue specificity - [original](https://davetang.org/muse/2013/08/28/tissue-specificity/) / [updated](tissue.html)
* Quantile normalisation in R - [original](https://davetang.org/muse/2014/07/07/quantile-normalisation-in-r/) / [updated](qn.html)
* Normalisation methods implemented in edgeR - [original](https://davetang.org/muse/2011/01/24/normalisation-methods-for-dge-data/) / [updated](edger.html)
* GSVA: gene set variation analysis - original / [updated](gsva.html)
* Using the cBioPortalData R package - original / [updated](cbioportal.html)
* Using the GenomicDataCommons package - original / [updated](gdc.html)
### Machine learning
* Getting started with tidymodels - original / [updated](tidymodels.html)
* Sequence composition and random forests - [original](https://davetang.org/muse/2013/09/14/sequence-composition-random-forests/) / [updated](tss_predict.html)
* Performance of binary classifiers - original / [updated](bin_class.html)
* Ordering Objects using Seriation in R - original / [updated](seriation.html)
### Programming
* Object-Oriented Programming - original / [updated](oo.html)
* Backticks in R - [original](https://davetang.org/muse/2022/09/07/backticks-in-r/) / [updated](r_backticks.html)
* Split single column of annotations into multiple columns - original / [updated](split_column.html)
* Matrix to adjacency list in R - [original](https://davetang.org/muse/2017/03/16/matrix-to-adjacency-list-in-r/) / [updated](adj_list.html)
* Using dplyr to aggregate in R - [original](https://davetang.org/muse/2016/10/13/using-dplyr-aggregate-r/) / [updated](dplyr_agg.html)
* Parallel computation in R - [original](https://davetang.org/muse/2016/11/04/parallel-distance-calculation/) / [updated](parallel.html)
* Reading irregular data into R - [original](https://davetang.org/muse/2023/06/02/reading-irregular-data-into-r/) / [updated](r_parsing.html)
* The tidyr pivot_longer and pivot_wider functions using base R - [original](https://davetang.org/muse/2023/07/26/the-tidyr-pivot_longer-and-pivot_wider-functions-using-base-r/) / [updated](reshape.html)
* Reading a list of files into a single R data frame - [original](https://davetang.org/muse/2023/06/23/reading-list-of-files-into-single-r-data-frame/) / [updated](read_files.html)
### Maths/Stats
* Monte Carlo integration - [original](https://davetang.org/muse/2020/10/09/monte-carlo-integration/) / [updated](monte_carlo.html)
* Set notation - [original](https://davetang.org/muse/2013/08/04/set-notation/) / [updated](set_notation.html)
* Step by step Principal Component Analysis using R [original](https://davetang.org/muse/2012/02/01/step-by-step-principal-components-analysis-using-r/) / [updated](pca.html)
* Distance Matrix Computation - [original](https://davetang.org/muse/2013/08/15/distance-matrix-computation/) / [updated](distance.html)
* Solving problems with graphs - [original](https://davetang.org/muse/2016/10/16/solving-problems-graphs/) / [updated](graph.html)
* Markov chain - [original](https://davetang.org/muse/2014/01/23/markov-chain/) / [updated](markov_chain.html)
* Hidden Markov Models - original / [updated](hmm.html)
### Misc
* Learning about antibodies - original / [updated](antibody.html)
* JSON versus YAML - original / [updated](json_vs_yaml.html)
* Working with HDF5 data in R - original / [updated](hdf5.html)
* Text mining using the tm package -original / [updated](tm.html)