Updates

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

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 index/es 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.

Started to keep track of updates

One thought on “Updates

  1. Pingback: Plotting error bars with RMusings from a PhD candidate

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