Last updated: 2024-10-23
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.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 2506265. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish
or
wflow_git_commit
). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: data/pbmc3k.csv
Ignored: data/pbmc3k.csv.gz
Ignored: data/pbmc3k/
Ignored: r_packages_4.4.0/
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
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 | 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.
seqinr
package - original
/ updated