Updates

General announcements (shown in bold) and a log of published posts that have been updated.

• 2023 October 11th: Updated my Tissue specificity post.
• 2023 July 12th: Updated my What do I use? post.
• 2023 June 6th: Updated my mapping qualities post to include BWA MEM.
• 2022 August 8th: Updated my Makefiles post with some additional notes.
• 2022 January 20th: Updated my BAM to CRAM post with a better example.
• 2020 February 26th: Updated GNU parallel post to show examples of stripping file extensions and directory paths.
• 2020 February 25th: Renewed domain for another two years.
• 2018 November 30th: People can now buy me a coffee to show some support 🙂
• 2018 November 8th: updated my Transcription factor binding site post to include HOMER; updated my pheatmap post to include saving a heatmap as a PNG file; and updated my ChIP-seq post to include a section on MACS2.
• 2018 May 15th: deactivated the Comment Reply Notification plugin, which was causing internal server errors. If visitors wish to be notified of replies to their comment, please check the Notify me of follow-up comments by email. checkbox when leaving a comment. In addition, I have deactivated the latex plugin because it was filling my error log with preg_replace(): The /e modifier is no longer supported, use preg_replace_callback instead in latex.php on line 47 and since WordPress now has native support.
• 2018 March 15th: Updated my edgeR normalisation post to include some Venn diagrams.
• 2017 November 30th: Updated my Distance Matrix Computation post to include negative distances.
• 2017 November 22nd: Updated post on fitting a Michaelis-Menten curve.
• 2017 November 17th: Updated my LaTeX post since WordPress now have native support; previously I was using a plugin.
• 2017 October 14th: Updated my tissue specificity post to be more coherent.
• 2017 September 7th: Updated my Comparing Distributions post to be more coherent.
• 2017 September 5th: Updated my manual linear regression post to use the women dataset in R instead of the Old Faithful Geyser dataset.
• 2016 September 15th: Updated my post on Getting started with the OMIM API to link to an R package I wrote for the OMIM API.
• 2015 October 12th: finally added a Creative Commons Attribution 4.0 International License to my blog.
• 2015 September 9th: Updated my really old post on PCA to include an analysis on the mtcars dataset.
• 2015 August 3rd: Updated GNU parallel post to demonstrate the use of Perl regular expressions for formatting the output.
• 2015 July 24th: my 200th post!
• 2015 April 6th: Updated my bare bone bedr R package to include another function.
• 2015 February 18th: Updated my twitteR post to reflect changes in the latest twitteR update.
• 2015 January 14th: Updated post on quantile normalisation to include a slide from Rafael, who taught the PH525x course.
• 2014 December 19th: Updated post on the Poisson distribution.
• 2014 December 19th: Updated post on the normal distribution.
• 2014 December 17th: Updated post on mapping qualities to include code used for the examples and made other improvements.
• 2014 December 12th: Updated post on normalisation methods implemented in edgeR.
• 2014 November 26th: Updated my R twitteR post to reflect changes in the tm package.
• 2014 October 8th: Updated clustering mapped reads post to include an example of clustering CAGE libraries from ENCODE.
• 2014 September 19th: Updated post on calculating the h-index to include a method that doesn't require sorting.
• 2014 September 19th: Updated my transpose post to compare my Perl code with datamash and some Python code.
• 2014 September 4th: Updated post on creating a sequence logo to include a script that parses the TRANSFAC matrix.dat file.
• 2014 August 11th: Created a blogroll.
• 2014 June 24th: Updated post on linear regression to use the Old Faithful dataset.
• 2014 June 21st: More explanatory information on my doing simple stuff in R post.
• 2014 June 20th: Used the iris dataset to demonstrate how to obtain basic statistics using R.
• 2014 June 18th: Cleaned up old post on defining genomic regions.
• 2014 June 8th: Updated an old post on Bowtie and multi-mapping reads.
• 2014 June 6th: Updated an old post on BWA and multi-mapping reads.
• 2014 June 5th: Updated post on using CPAT, elaborating on the features used to calculate the coding potential.
• 2014 May 14th: Added more tips to my small list of command line tips.
• 2014 May 7th: Updated my Caesar cipher in Perl with a slightly better version.
• 2014 April 18th: Updated the post on variance in RNA-Seq data and the post on edgeR's common dispersion.
• 2014 March 14th: Updated post on using ENCODE ChIA-PET data to include circos plot of long range chromosomal interactions on chromosome one.
• 2014 March 6th: Updated my Student Journal Club post to include a link to my Wiki page that provides summaries of papers I've read.
• 2014 March 6th: I just realised that the Gist GitHub Shortcode plugin was broken and all the code wasn't showing! Turns out WordPress now has support for showing Gist code; simply just paste the URL. I hope I have amended all the broken shortcodes.
• 2014 February 13th: Updated my About page with a link to my résumé.
• 2014 January 27th: Updated my post on comparing R, Python and Perl syntax by including syntax for conditionals.
• 2014 January 7th: Updated my distance matrix post to include a Mantel test, which can be used to calculate the correlation between two distance matrices.
• 2014 January 6th: Updated post on Creating a correlation matrix with R to show one way of parallelising the calculations and showed code for creating a network within R.
• 2014 January 2nd: Major re-write of the Using the ENCODE methylation data post.
• 2013 December 17th: Updated post on using Transcription Factor Binding Site prediction tools to include the JASPAR database for running TESS.
• 2013 December 17th: Updated post on using the ENCODE RRBS data by correctly using the read counts and methylation percent.
• 2013 December 16th: Updated post on checking whether two genes belong to the same pathway to include code for using the Reactome database.
• 2013 December 13th: Updated my coverage plot post to include code for focusing on a specific region. 2013 November 28th: Updated my GenomicRanges post to show an example of creating a data frame that associates the overlapping elements.
• 2013 November 25th: Updated my Using aggregate and apply in R post to use the dataset available as part of R.
• 2013 November 23rd: Updated my Gene Ontology Enrichment Analysis post to include the use of biomaRt and added an analysis using topGO.
• 2013 November 20th: Fixed commenting system, which was probably broken for a while (I thought it was a bit too quiet).
• 2013 November 20th: Updated my coverage plot in R post to include a coverage plot in the form of a histogram.
• 2013 November 20th: Updated my Tabix post to include instructions for creating a tabix index of lots of BAM files and showing the correct method of slicing out a portion of reads in a BAM file.
• 2013 November 15th: Updated my Gviz post to include the visualisation of almost 1,000 bam files.
• 2013 November 12th: Updated my How deep should we sequence post to use the latest version of preseq, which can model extremely sparse datasets.
• 2013 November 12th: Updated my Using ENCODE methylation data post to include a link to the ENCODE WGBS GEO archive.
• 2013 November 11th: Updated my Doing simple stuff in R post to include finding the specific indexes of matrix, whereby the value satisfies a condition.
• 2013 November 10th: Updated my Setting up Windows for bioinformatics post to include updated links.
• 2013 November 7th: Updated my Gviz post to include the visualisation of bam files.
• 2013 November 5th: Updated my using blat to map short RNAs post to include the mapping of human piRNAs.
• 2013 November 5th: Updated my post on using the seqinr package in R to include code for outputting sequence into a fasta file.
• 2013 November 5th: Updated my Top 10 page to include the RGoogleAnalytics analysis used for calculating the most highly accessed posts.
• 2013 November 5th: Updated my About page to encourage people to use Twitter.
• 2013 September 12th: Updated my Random forests post on predicting different wines to include an area under the curve (AUC) analysis and Started to keep track of updates.