25 October 2024
Plot a phylogenetic tree with bokeh and biopython
04 June 2024
Bacterial species identification from WGS using 16S genes
31 May 2024
Plot and colour a minimum spanning tree with networkx
30 May 2024
An updated convenience function for ggtree with heatmaps
29 March 2024
Calculate PubMLST sequence types using Python
22 March 2024
Two quick ways of building a bacterial species phylogeny
28 January 2024
Filtering a QTableView with QSortFilterProxyModel
21 January 2024
Finding genes in a genome or assembly with Python
19 January 2024
Fetch assemblies and associated biosample data using Entrez tools with Biopython
05 January 2024
Excess mortality in Ireland still high in 2023
29 December 2023
A Panel app for image-to-image generation
18 December 2023
image-to-image with Stable Diffusion in Python
12 November 2023
Speech diarization with OpenAI whisper and pyannote.audio
21 September 2023
Condition Stable Diffusion images with ControlNet
19 September 2023
AI art with Stable Diffusion in Python
15 September 2023
SNP clustering and type naming of pathogens from WGS
18 June 2023
A phylogenetic tree viewer with PyQt and ToyTree
22 March 2023
Simulate land parcels and fragmentation with geopandas
19 March 2023
An individual based model of farm pathogen spread with Python/Mesa
15 March 2023
Make a contact network from a geopandas geodataframe
23 January 2023
Make networkx Delaunay graphs from geopandas dataframes
14 January 2023
Using Molecular Nodes in Blender to visualise proteins
29 December 2022
Scrape dynamic tables in Python with Playwright
21 December 2022
Can ChatGPT solve bioinformatic problems with Python?
19 December 2022
DALLE-2 and AI generated art.
15 October 2022
How to host your podcast with github
08 September 2022
Excess mortality in Ireland is still high in 2022
13 August 2022
Mapping the historical development of Tallaght
07 August 2022
Plotting gridded quantitative data with geopandas - Irish forestry
04 August 2022
Make regular grids from polygons with geopandas
02 August 2022
Plot phylogenies with annotation in R using ggtree and gheatmap
10 April 2022
Parallelize a function in Python that returns a pandas DataFrame
28 March 2022
batchfilerename - A simple utility for batch file renaming
20 March 2022
Using IGV inside Jupyter Lab notebooks
23 February 2022
Scrape paginated tables in Python with beautifulsoup
29 January 2022
Ireland mortality data from RIP.ie, updated for 2021
12 January 2022
Pandemic restrictions have caused misery in low income countries
14 November 2021
High vaccination rates don't prevent transmission of SARS-CoV-2
12 November 2021
Seasonality of SARS-CoV-2
18 October 2021
Bacterial SNP detection with nanopore vs. illumina sequencing
03 September 2021
Natural immunity to SARS-CoV-2
10 July 2021
Comparison of SNP detection using duplicate sequencing runs in SNiPgenie
19 June 2021
wgMLST vs the reference-align-SNP-calling method for M.bovis
15 June 2021
Deaths in Ireland from RIP.ie - another look
10 June 2021
A whole genome MLST (wgMLST) implementation in Python
18 May 2021
Viewing the THOR dataset with Bokeh and Panel
15 May 2021
The scale of US bombing in Southeast Asia revealed in the THOR dataset
26 February 2021
A phylogenetic tree viewer with Qt and Toytree
16 February 2021
A simple GIS plugin for Tablexplore
28 January 2021
Ireland deaths in 2019/2020 compared to previous years
25 January 2021
Daily deaths in Ireland from RIP.ie in 2019 and 2020
20 January 2021
Visualizing Irish girls names since 1970
15 January 2021
M. bovis spoligotyping from WGS reads
11 January 2021
Linux application packaging and universal formats
23 December 2020
Detecting polymorphisms in the RD900 region of MTBC species
19 December 2020
Tablexplore - a desktop tool for table analysis
29 November 2020
Epidemics, PCR and the dangers of mass testing
28 November 2020
Convert a multi-sample VCF to a pandas DataFrame
15 November 2020
A network agent based infection model with Mesa
10 November 2020
Find PFAM domains in protein sequences with Python
02 November 2020
Covid-19 and T cell immunity
28 October 2020
Estimating Irelands tree coverage with QGIS and GeoPandas
18 October 2020
Build an exe using pyinstaller with GitHub Actions
06 October 2020
A simple image gallery in Jekyll without plugins
05 September 2020
An MHC-Class I binding predictor with sklearn, part 2
18 August 2020
Ireland COVID-19 trend in positive rate
15 August 2020
Predicting cross-reactive T cell epitopes in Sars-CoV-2
06 August 2020
COVID tracking project - tests vs positive rates
24 July 2020
Death causes in England and Wales comparison - Winton Centre
21 July 2020
Sequence alignment viewer with Qt/PySide2
11 July 2020
Eurostat deaths from all causes dataset plots
07 July 2020
pathogenie - A desktop application for microbial genome annotation
19 May 2020
Fasta alignment from a multi sample VCF - a less terrible method
12 May 2020
SNiPgenie - a tool for SNP site detection from NGS data
28 April 2020
Simple MTBC regions of difference analysis with Python
19 April 2020
Finding all amino acid mutations in SARS-CoV-2
14 April 2020
A simple agent based infection model with Mesa and Bokeh
07 April 2020
Create a fasta alignment from a multi sample VCF
01 April 2020
COVID-19 ECDC data dashboard with Panel
28 March 2020
COVID-19 ECDC data plots with Bokeh
18 March 2020
Run bcftools mpileup in parallel with Python
11 March 2020
Deploy a Python application with snapcraft
02 March 2020
Model of the SARS-CoV-2 spike protein in Blender
28 February 2020
Explore the SARS-CoV-2 spike protein sequences using Python tools
18 February 2020
Updates to a genome annotation on the ENA via Webin-CLI
05 February 2020
Plot fastq file metrics with Python
30 January 2020
Compile windows exe files with MSYS2
25 January 2020
A simple genome browser with Qt and dna_features_viewer
06 January 2020
Interactive plots of World development indicators with Panel
03 January 2020
Concurrent processes in PySide2/PyQt5 applications
14 December 2019
Genome annotation with BLAST, Prodigal and Biopython
29 November 2019
Embed Bokeh plots in Jekyll markdown
28 November 2019
Categorical region plots with geopandas
15 November 2019
Choropleth maps with geopandas, Bokeh and Panel
05 November 2019
Analysis of MTBC regions of difference with NucDiff
20 October 2019
Rapid Average Nucleotide Identity calculation with FastANI
13 October 2019
NucDiff for bacterial whole genome comparisons
30 September 2019
Plotting global sea ice extent data with four different Python packages
24 September 2019
Interactively view datasets with HoloViews
15 September 2019
Javascript callbacks for linking bokeh plots to panel widgets
31 August 2019
Retrieving genome assemblies via Entrez with Python
12 August 2019
Accessing data from the PDB with Python
22 July 2019
Bioinformatics on the Raspberry Pi 4
11 July 2019
A sequence alignment viewer with Bokeh and Panel
02 July 2019
Dashboards with PyViz Panel for interactive web apps
17 May 2019
Predicting neoantigens
04 April 2019
Make protein models with Blender
20 March 2019
Sequence, gene and protein databases: are you confused?
27 February 2019
Unknown proteins in Mycobacterium tuberculosis
25 February 2019
Reading and writing genbank/embl files with Python
25 November 2018
Using epitopepredict for MHC binding prediction in Python
12 November 2018
Create an MHC-Class I binding predictor in Python
09 October 2018
Creating a local RefSeq protein blast database
14 August 2018
Create a bacterial GFF from a genbank file for BCFtools/csq
05 July 2017
DataExplore - grouped plots in version 0.8.0
11 December 2015
Example: plotting miRNA abundance data (advanced)
15 September 2015
Looking at the Titanic dataset
18 July 2015
Zenodo and sharing your software
14 June 2015
Educational software for data analysis
11 June 2015
DataExplore Features
30 May 2015
DataExplore Introduction
//mathjax