Last updated: 2024-12-24

Checks: 2 0

Knit directory: muse/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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Repository version: f0f7a57

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd f0f7a57 Dave Tang 2024-12-24 Finding Markers with Seurat
html b616e4e Dave Tang 2024-11-28 Build site.
Rmd 989fe1c Dave Tang 2024-11-28 Benjamini-Hochberg correction
html 2c080dc Dave Tang 2024-11-01 Build site.
Rmd 124a8d9 Dave Tang 2024-11-01 Using clusterProfiler
html 6e8540e Dave Tang 2024-10-24 Build site.
Rmd ff049cd Dave Tang 2024-10-24 Using biomaRt
html de5bf16 Dave Tang 2024-10-23 Build site.
Rmd 2506265 Dave Tang 2024-10-23 Using AnnotationDbi
html a658556 Dave Tang 2024-10-23 Build site.
Rmd e471135 Dave Tang 2024-10-23 edgeR versus DESeq2
html c9037d1 Dave Tang 2024-10-22 Build site.
Rmd f7369ce Dave Tang 2024-10-22 Differential gene expression analysis using edgeR
html bb3c51c Dave Tang 2024-08-29 Build site.
Rmd 128229e Dave Tang 2024-08-29 Non-invasive pretty printing of R code
html b9f957f Dave Tang 2024-08-29 Build site.
Rmd f4c0b1d Dave Tang 2024-08-29 Benchmarking R expressions
html b023be3 Dave Tang 2024-08-16 Build site.
Rmd cf1ff46 Dave Tang 2024-08-16 k-methods clustering
html 850c62d Dave Tang 2024-08-16 Build site.
Rmd ad9ead7 Dave Tang 2024-08-16 Hierarchical clustering
html 4ec2479 Dave Tang 2024-08-07 Build site.
Rmd 7f9058a Dave Tang 2024-08-07 Generative models
html 365890e Dave Tang 2024-08-05 Build site.
html 1383bf7 Dave Tang 2024-08-05 Build site.
Rmd d5e67bc Dave Tang 2024-08-05 Getting started with DESeq2
html e49a794 Dave Tang 2024-07-30 Build site.
Rmd 2dceb55 Dave Tang 2024-07-30 The Poisson distribution
html c34f664 Dave Tang 2024-07-29 Build site.
Rmd 0c10121 Dave Tang 2024-07-29 Normalisation methods using edgeR
html 1dbd4f3 Dave Tang 2024-07-25 Build site.
Rmd 39a6fe8 Dave Tang 2024-07-25 Querying the SRA
html 6917788 Dave Tang 2024-07-17 Build site.
Rmd bb8ad42 Dave Tang 2024-07-17 Database basics
html 1d3b697 Dave Tang 2024-07-17 Build site.
Rmd 1b02e91 Dave Tang 2024-07-17 Getting started with the R arrow package
html ea0424a Dave Tang 2024-07-17 Build site.
Rmd d754f94 Dave Tang 2024-07-17 Downloading files using the curl package
html af2bef5 Dave Tang 2024-06-19 Build site.
Rmd f08c5d1 Dave Tang 2024-06-19 R function for calculating confusion matrix rates
html 0d55a75 Dave Tang 2024-06-19 Build site.
Rmd 19fb6e6 Dave Tang 2024-06-19 Rand Index versus Adjusted Rand Index
html 585ebe4 Dave Tang 2024-06-19 Build site.
Rmd 0c163e0 Dave Tang 2024-06-19 Adjusted Rand Index
html 01c75b7 Dave Tang 2024-06-19 Build site.
Rmd 77a8ff4 Dave Tang 2024-06-19 The Rand index
html cd09128 Dave Tang 2024-04-20 Build site.
Rmd 1a7c3c1 Dave Tang 2024-04-20 Linear algebra basics
html 687dd2e Dave Tang 2024-04-20 Build site.
Rmd 16d27ab Dave Tang 2024-04-20 Rebuild index
Rmd 593742d Dave Tang 2024-04-20 Fix conflict
html 593742d Dave Tang 2024-04-20 Fix conflict
html eaa681b Dave Tang 2024-04-20 Build site.
Rmd 8c5bc97 Dave Tang 2024-04-20 Euclidean vs. Cosine
html 46648d5 Dave Tang 2024-04-15 Build site.
Rmd d193658 Dave Tang 2024-04-15 CCA
Rmd dfeb2c6 Dave Tang 2024-04-14 Fix merge conflict
html dfeb2c6 Dave Tang 2024-04-14 Fix merge conflict
html 9abb7b6 Dave Tang 2024-04-14 Build site.
Rmd 72ffea9 Dave Tang 2024-04-14 Getting started with harmony
html e911e7c Dave Tang 2024-04-10 Build site.
Rmd 7fac102 Dave Tang 2024-04-10 Creating a correlation matrix with R
html 164872b Dave Tang 2024-04-08 Build site.
Rmd b3568c0 Dave Tang 2024-04-08 CELLxGENE Census
html 944e5f2 Dave Tang 2024-03-19 Build site.
Rmd ae0ea42 Dave Tang 2024-03-19 Getting started with Seurat
html 5524d3e Dave Tang 2023-12-18 Build site.
Rmd ae829e2 Dave Tang 2023-12-18 Remove duplicate link
html 4241975 Dave Tang 2023-12-13 Build site.
Rmd 5b0e194 Dave Tang 2023-12-13 Downloading molecular signatures in R
html 81a9b10 Dave Tang 2023-11-24 Build site.
Rmd a55e367 Dave Tang 2023-11-24 Getting started with Cell Ranger
html b1d68db Dave Tang 2023-11-09 Build site.
Rmd 16f2e4c Dave Tang 2023-11-09 Survival analysis
html 4011b46 Dave Tang 2023-11-02 Build site.
Rmd 5acae29 Dave Tang 2023-11-02 Text mining using the tm package
html 7b31570 Dave Tang 2023-11-01 Build site.
Rmd 3e13eb5 Dave Tang 2023-11-01 ComplexHeatmap
html 8fca622 Dave Tang 2023-11-01 Build site.
Rmd 3fc037e Dave Tang 2023-11-01 Using the GenomicDataCommons package
html 8072645 Dave Tang 2023-11-01 Build site.
Rmd 9bf5d39 Dave Tang 2023-11-01 cBioPortal
html b0af093 Dave Tang 2023-10-23 Build site.
Rmd aeb90e1 Dave Tang 2023-10-23 GSVA
html 332f663 Dave Tang 2023-10-19 Build site.
Rmd c0079b2 Dave Tang 2023-10-19 Plot networks using Plotly
html d2bad6a Dave Tang 2023-10-13 Build site.
Rmd 8ffc69d Dave Tang 2023-10-13 More random numbers
html 861b1fe Dave Tang 2023-10-13 Build site.
Rmd d6a644a Dave Tang 2023-10-13 Organise posts
html 67bf9ca Dave Tang 2023-10-13 Build site.
Rmd 4bc5f6a Dave Tang 2023-10-13 edgeR normalisation
html f715b16 Dave Tang 2023-10-12 Build site.
Rmd 1ede478 Dave Tang 2023-10-12 Quantile normalisation
html d5f2d49 Dave Tang 2023-10-11 Build site.
Rmd 7c1bdcd Dave Tang 2023-10-11 Tissue specificity
html 2e62b65 Dave Tang 2023-10-05 Build site.
Rmd a63df84 Dave Tang 2023-10-05 Ordering objects using seriation
html 5f5ccc4 Dave Tang 2023-09-06 Build site.
Rmd e02b689 Dave Tang 2023-09-06 Set notation
html 5cdedf4 Dave Tang 2023-08-01 Build site.
Rmd b29e9ec Dave Tang 2023-08-01 Object-Oriented Programming
html ccc5fa4 Dave Tang 2023-07-26 Build site.
Rmd b5c3509 Dave Tang 2023-07-26 Read list of files
html a36c3f2 Dave Tang 2023-07-26 Build site.
Rmd c9869c6 Dave Tang 2023-07-26 Link to davetang.org/muse
html 3e572d6 Dave Tang 2023-07-26 Build site.
Rmd bd5654d Dave Tang 2023-07-26 Convert wide and long data
html f706b10 Dave Tang 2023-07-21 Build site.
Rmd e5a16af Dave Tang 2023-07-21 HDF5
html c019f75 Dave Tang 2023-07-13 Build site.
Rmd e9ca6f1 Dave Tang 2023-07-13 Update index
html 8090882 Dave Tang 2023-06-29 Build site.
Rmd a3c61e8 Dave Tang 2023-06-29 Hidden Markov Models
html 76621f1 Dave Tang 2023-06-28 Build site.
Rmd d944430 Dave Tang 2023-06-28 Position weight matrix
html b707032 Dave Tang 2023-06-26 Build site.
Rmd 9161c86 Dave Tang 2023-06-26 Learning about antibodies
html f8fc2f2 Dave Tang 2023-06-02 Build site.
Rmd 140c2a0 Dave Tang 2023-06-02 Update post
html 27ea248 Dave Tang 2023-05-30 Build site.
Rmd 7432d2f Dave Tang 2023-05-30 Parsing irregular formats
html 3bb3245 Dave Tang 2023-05-19 Build site.
Rmd 50c92d7 Dave Tang 2023-05-19 JSON and YAML formats
html e1a9ff4 Dave Tang 2023-03-10 Build site.
Rmd beec955 Dave Tang 2023-03-10 Fix link
html dbaa54d Dave Tang 2023-03-10 Build site.
Rmd 4df0a4b Dave Tang 2023-03-10 Performance of binary classifiers
html eac5905 Dave Tang 2023-02-13 Build site.
Rmd 28276f9 Dave Tang 2023-02-13 Using ensembldb
html 0a435d1 Dave Tang 2023-02-13 Build site.
Rmd 1242888 Dave Tang 2023-02-13 GenomicRanges
html 0b4b03d Dave Tang 2023-02-09 Build site.
Rmd fdf7aee Dave Tang 2023-02-09 Hyperlink typo
html 49d4629 Dave Tang 2023-02-09 Build site.
Rmd 0c22d6a Dave Tang 2023-02-09 Solving problems with graphs
html b82b4fc Dave Tang 2023-02-01 Build site.
Rmd fb91538 Dave Tang 2023-02-01 fgsea example data
html add50fe Dave Tang 2022-12-12 Build site.
Rmd 419613a Dave Tang 2022-12-12 Tidymodels
html 130d11f Dave Tang 2022-11-17 Build site.
Rmd b2043f3 Dave Tang 2022-11-17 Parallel computation in R
html 7a6571a Dave Tang 2022-11-04 Build site.
Rmd 6def24c Dave Tang 2022-11-04 Adjacency list
html 6bbf281 Dave Tang 2022-10-20 Build site.
Rmd f9bfcec Dave Tang 2022-10-20 PCA
html 8107082 Dave Tang 2022-09-07 Build site.
Rmd 0a02109 Dave Tang 2022-09-07 Backticks in R
html b814eb1 Dave Tang 2022-04-28 Build site.
Rmd 9b739a1 Dave Tang 2022-04-28 Using the seqinr package
html b743be8 Dave Tang 2022-04-26 Build site.
Rmd 9ae1c27 Dave Tang 2022-04-26 Aggregation with dplyr
html 1229a49 Dave Tang 2022-04-22 Build site.
Rmd 8e4bd29 Dave Tang 2022-04-22 Fix bullet point
html fd41c75 Dave Tang 2022-04-22 Build site.
Rmd e372c81 Dave Tang 2022-04-22 TSS
html d334dbd Dave Tang 2022-04-14 Build site.
Rmd a9f5e22 Dave Tang 2022-04-14 Distance metrics
html d6644d2 Dave Tang 2021-06-22 Build site.
Rmd 8ae8e21 Dave Tang 2021-06-22 Post on splitting a single column of annotations
html 1cd1577 davetang 2021-01-27 Build site.
Rmd 687a6ca davetang 2021-01-27 Gene Ontology Enrichment Analysis
html 6ef7a62 davetang 2020-12-01 Build site.
Rmd acb1733 davetang 2020-12-01 Read GTF files into R
html e8c8661 davetang 2020-11-15 Build site.
Rmd ab3533f davetang 2020-11-15 Fix link
html 5dc50c6 davetang 2020-11-15 Build site.
Rmd 9639627 davetang 2020-11-15 Complex UpSet plots
html 2db13ea davetang 2020-11-10 Build site.
Rmd 268312f davetang 2020-11-10 wflow_publish(files = c("analysis/index.Rmd", "analysis/google_trends.Rmd",
html 03f05e8 davetang 2020-10-18 Build site.
Rmd f79342a davetang 2020-10-18 Markov chain post
html 586b91f Dave Tang 2020-07-12 Build site.
Rmd b1d6edd Dave Tang 2020-07-12 pheatmap
Rmd b3f3dc1 Dave Tang 2020-07-12 Start workflowr project.

I refer to my blog 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 / updated
  • Visualising Google Trends results with R - original / updated
  • Complex UpSet plots - original / updated
  • Gene expression heatmap using ARCHS4 data - original / updated
  • Network graph using R Plotly - original / updated
  • Making a heatmap in R with the ComplexHeatmap package - original / updated

Bioinformatics

  • Read GTF file into R - original / updated
  • Gene Ontology Enrichment Analysis - original / updated
  • Using the R seqinr package - original / updated
  • Using the Bioconductor ensembldb package - original / updated
  • Using the fast preranked gene set enrichment analysis (fgsea) package - original / updated
  • Using the Bioconductor GenomicRanges package - original / updated
  • Position weight matrix - original / updated
  • Tissue specificity - original / updated
  • Quantile normalisation in R - original / updated
  • Normalisation methods implemented in edgeR - original / updated
  • GSVA: gene set variation analysis - original / updated
  • Using the cBioPortalData R package - original / updated
  • Using the GenomicDataCommons package - original / updated
  • Getting started with Cell Ranger - original / updated
  • Downloading molecular signatures from MSigDB in R - original / updated
  • Getting started with Seurat - original / updated
  • Getting started with CELLxGENE Discover Census - original / updated
  • Getting started with harmony - original / updated
  • Interfacing with the Sequence Read Archive in R - original / updated
  • Differential gene expression analysis with DESeq2 - original / updated
  • Differential gene expression analysis using edgeR - original / updated
  • edgeR versus DESeq2 - original / updated
  • Bioconductor annotation packages - original / updated
  • Learning to use biomaRt - original / updated
  • Getting started with clusterProfiler - original / updated
  • Finding Markers with Seurat - original / updated

Machine learning

  • Getting started with tidymodels - original / updated
  • Sequence composition and random forests - original / updated
  • Performance of binary classifiers - original / updated
  • Ordering Objects using Seriation in R - original / updated
  • R function for calculating confusion matrix rates - original / updated

Programming

Maths/Stats

Misc

  • Learning about antibodies - original / updated
  • JSON versus YAML - original / updated
  • Working with HDF5 data in R - original / updated
  • Text mining using the tm package - original / updated
  • Downloading files using the curl package - original / updated
  • Getting started with the R arrow package - original / updated
  • Interfacing with databases in R - original / updated