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