Paul Harrison

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Home page of Dr. Paul Harrison. I work for the Monash Bioinformatics Platform.

pfh@logarithmic.net

@paulfharrison

PGP public key
Fingerprint B829 F851 00B7 9CB7 6897 DCA7 A881 5DA8 5150 5ABF

Bioinformatics software

Langevitour: Javascript with R wrapper. Interactively tour a high-dimensional numeric dataset at 60 FPS. Uses small motions to convey which points are near each other.

Topconfects: Bioconductor R package. Top differential expression by confident effect size. A more intuitive way to use "TREAT".

Weitrix: Bioconductor R package. Tools for working with a matrix of data measured with varying precision or with missing values.

Varistran: R package. Variance stabilizing transformation for RNA-Seq data. This is a useful pre-processing step prior to visualization, and also makes clustering and statistical analysis more straightforward. Includes a shiny app for assessing RNA-seq data quality with heatmap and biplot.

Tail-Tools: Analysis pipeline for PAT-Seq data.

Nesoni: Tools for processing bacterial high-throughput sequencing data. (No longer maintained.)

Plasmodium Autocount and Semiautocount: Cell counting on blood smears. (Historical interest only, use a convolutional neural network.)


Talks and slides

Langevitour
2022-03-25 slides Short talk for the NUMBATS group.
2022-06-22 video slides useR! Conference talk.
2022-09-20 slides ABACBS National Seminars talk.

Weitrix
2020-10-12 slides Weitrix: calibrate precision weights for diverse types of data in a matrix, explore and test weighted or sparse data (for Bioconductor Asia 2020).]
2020-11-04 video

Topconfects
2019-08-21 slides An introduction for a general audience (for the NUMBATS group).
2020-03-10 slides A more technical presentation (WEHI Bioinformatics Seminar).

Machine learning
2017-06-14 slides Introduction to logistic regression and decision trees, and a description of my Melbourne Datathon 2017 Kaggle entry

Tiling patterns
2022-01-27 video slides Mathematical weirdness in tiling patterns.


Writing

Publications on Google Scholar.

PhD thesis (2005) on image texture synthesis. I also have several publications relating to my PhD work on texture.

Introduction to R, version 2 (2018) (version 1 here) Workshop material introducing R.

Programming and tidy data analysis in R (2019) (based on an ealier workshop R more (2016)). Workshop to go from beginner to intermediate R usage, which I have developed and presented with other members of the Monash Bioinformatics Platform and the Monash Data Fluency initiative.

Linear models in R (2018) Workshop material introducing linear models in R. Linear models are a very broadly useful statistical tool, and also necessary background knowledge for using Bioconductor packages such as limma.

Dance of the CIs, a Javascript app version of the "Dance of the CIs" from the "New Statistics". Illustrates the meaning of confidence intervals, standard error, standard deviation, and prediction intervals.

>> Fun and personal stuff




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