Tags
- dataexplore 1
- miRNA 1
- merge 1
- melt 1
- seaborn 3
- plotting 9
- bcftools/csq 1
- refseq 1
- mhc 3
- epitopepredict 1
- annotation 5
- genbank 3
- python 60
- mtb 2
- ensembl 1
- ncbi 1
- protein 1
- blender 3
- epitope 2
- neoantigen 1
- cancer 1
- immunotherapy 1
- pyviz 7
- bokeh 8
- pi4 1
- bwa 1
- pdb 1
- holoviews 1
- matplotlib 1
- arctic 1
- nucdiff 1
- microbiology 12
- genomics 27
- ani 1
- mtbc 6
- mtbdiff 1
- maps 11
- panel 4
- geopandas 7
- pyside2 7
- wdi 1
- windows 1
- ngs 6
- sarscov2 5
- snapcraft 2
- covid19 11
- abm 3
- mesa 3
- eurostat 1
- immunology 1
- jekyll 2
- github 2
- forestry 1
- PySide2 1
- tablexplore 2
- linux 1
- cso 3
- toytree 1
- THOR 2
- rip.ie 4
- snipgenie 3
- nanopore 1
- phylogeny 1
- ai 6
- pyqt 1
dataexplore
miRNA
merge
melt
seaborn
- Death causes in England and Wales comparison - Winton Centre
- Eurostat deaths from all causes dataset plots
- Example: plotting miRNA abundance data (advanced)
plotting
- Plot phylogenies with annotation in R using ggtree and gheatmap
- Ireland mortality data from RIP.ie, updated for 2021
- 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
- Visualizing Irish girls names since 1970
- DataExplore - grouped plots in version 0.8.0
bcftools/csq
refseq
mhc
- An MHC-Class I binding predictor with sklearn, part 2
- Using epitopepredict for MHC binding prediction in Python
- Create an MHC-Class I binding predictor in Python
epitopepredict
annotation
- Find PFAM domains in protein sequences with Python
- pathogenie - A desktop application for microbial genome annotation
- A simple genome browser with Qt and dna_features_viewer
- Unknown proteins in Mycobacterium tuberculosis
- Reading and writing genbank/embl files with Python
genbank
- Retrieving genome assemblies via Entrez with Python
- Sequence, gene and protein databases: are you confused?
- Reading and writing genbank/embl files with Python
python
- Calculate PubMLST sequence types using Python
- Two quick ways of building a bacterial species phylogeny
- Filtering a QTableView with QSortFilterProxyModel
- Finding genes in a genome or assembly with Python
- Fetch assemblies and associated biosample data using Entrez tools with Biopython
- 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
- SNP clustering and type naming of pathogens from WGS
- A phylogenetic tree viewer with PyQt and ToyTree
- 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
- Make networkx Delaunay graphs from geopandas dataframes
- Scrape dynamic tables in Python with Playwright
- Can ChatGPT solve bioinformatic problems with Python?
- Excess mortality in Ireland is still high in 2022
- Mapping the historical development of Tallaght
- Plotting gridded quantitative data with geopandas - Irish forestry
- Make regular grids from polygons with geopandas
- Parallelize a function in Python that returns a pandas DataFrame
- batchfilerename - A simple utility for batch file renaming
- Using IGV inside Jupyter Lab notebooks
- Scrape paginated tables in Python with beautifulsoup
- Ireland mortality data from RIP.ie, updated for 2021
- 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
- Deaths in Ireland from RIP.ie - another look
- A whole genome MLST (wgMLST) implementation in Python
- Visualizing Irish girls names since 1970
- M. bovis spoligotyping from WGS reads
- Detecting polymorphisms in the RD900 region of MTBC species
- Convert a multi-sample VCF to a pandas DataFrame
- Build an exe using pyinstaller with GitHub Actions
- 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
- Create a fasta alignment from a multi sample VCF
- COVID-19 ECDC data dashboard with Panel
- COVID-19 ECDC data plots with Bokeh
- Run bcftools mpileup in parallel with Python
- Plot fastq file metrics with Python
- A simple genome browser with Qt and dna_features_viewer
- Interactive plots of World development indicators with Panel
- Concurrent processes in PySide2/PyQt5 applications
- 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
- Retrieving genome assemblies via Entrez with Python
- Accessing data from the PDB with Python
- A sequence alignment viewer with Bokeh and Panel
- Dashboards with PyViz Panel for interactive web apps
- Reading and writing genbank/embl files with Python
mtb
ensembl
ncbi
protein
blender
- Using Molecular Nodes in Blender to visualise proteins
- Model of the SARS-CoV-2 spike protein in Blender
- Make protein models with Blender
epitope
neoantigen
cancer
immunotherapy
pyviz
- COVID-19 ECDC data dashboard with Panel
- Interactive plots of World development indicators with Panel
- 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
- A sequence alignment viewer with Bokeh and Panel
- Dashboards with PyViz Panel for interactive web apps
bokeh
- Viewing the THOR dataset with Bokeh and Panel
- COVID-19 ECDC data dashboard with Panel
- COVID-19 ECDC data plots with Bokeh
- Embed Bokeh plots in Jekyll markdown
- Choropleth maps with geopandas, Bokeh and Panel
- Plotting global sea ice extent data with four different Python packages
- Javascript callbacks for linking bokeh plots to panel widgets
- A sequence alignment viewer with Bokeh and Panel
pi4
bwa
pdb
holoviews
matplotlib
arctic
nucdiff
microbiology
- SNP clustering and type naming of pathogens from WGS
- Using IGV inside Jupyter Lab notebooks
- 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
- Simple MTBC regions of difference analysis with Python
- Genome annotation with BLAST, Prodigal and Biopython
- Analysis of MTBC regions of difference with NucDiff
- Rapid Average Nucleotide Identity calculation with FastANI
- NucDiff for bacterial whole genome comparisons
genomics
- 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 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
- 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
- Finding all amino acid mutations in SARS-CoV-2
- 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
- Plot fastq file metrics with Python
- A simple genome browser with Qt and dna_features_viewer
- Genome annotation with BLAST, Prodigal and Biopython
- Rapid Average Nucleotide Identity calculation with FastANI
ani
mtbc
- 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
- Simple MTBC regions of difference analysis with Python
- Analysis of MTBC regions of difference with NucDiff
mtbdiff
maps
- Simulate land parcels and fragmentation with geopandas
- Make a contact network from a geopandas geodataframe
- Make networkx Delaunay graphs from geopandas dataframes
- Mapping the historical development of Tallaght
- Plotting gridded quantitative data with geopandas - Irish forestry
- Make regular grids from polygons with geopandas
- A simple GIS plugin for Tablexplore
- Estimating Irelands tree coverage with QGIS and GeoPandas
- Embed Bokeh plots in Jekyll markdown
- Categorical region plots with geopandas
- Choropleth maps with geopandas, Bokeh and Panel
panel
- Viewing the THOR dataset with Bokeh and Panel
- A network agent based infection model with Mesa
- Interactive plots of World development indicators with Panel
- Choropleth maps with geopandas, Bokeh and Panel
geopandas
- Simulate land parcels and fragmentation with geopandas
- Make a contact network from a geopandas geodataframe
- Make networkx Delaunay graphs from geopandas dataframes
- Mapping the historical development of Tallaght
- Plotting gridded quantitative data with geopandas - Irish forestry
- Make regular grids from polygons with geopandas
- Categorical region plots with geopandas
pyside2
- Filtering a QTableView with QSortFilterProxyModel
- A phylogenetic tree viewer with Qt and Toytree
- Sequence alignment viewer with Qt/PySide2
- pathogenie - A desktop application for microbial genome annotation
- SNiPgenie - a tool for SNP site detection from NGS data
- A simple genome browser with Qt and dna_features_viewer
- Concurrent processes in PySide2/PyQt5 applications
wdi
windows
ngs
- Convert a multi-sample VCF to a pandas DataFrame
- Fasta alignment from a multi sample VCF - a less terrible method
- SNiPgenie - a tool for SNP site detection from NGS data
- Create a fasta alignment from a multi sample VCF
- Run bcftools mpileup in parallel with Python
- Plot fastq file metrics with Python
sarscov2
- Epidemics, PCR and the dangers of mass testing
- Predicting cross-reactive T cell epitopes in Sars-CoV-2
- Finding all amino acid mutations in SARS-CoV-2
- Model of the SARS-CoV-2 spike protein in Blender
- Explore the SARS-CoV-2 spike protein sequences using Python tools
snapcraft
covid19
- 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
- Epidemics, PCR and the dangers of mass testing
- Covid-19 and T cell immunity
- Ireland COVID-19 trend in positive rate
- COVID tracking project - tests vs positive rates
- Death causes in England and Wales comparison - Winton Centre
- COVID-19 ECDC data dashboard with Panel
- COVID-19 ECDC data plots with Bokeh
abm
- An individual based model of farm pathogen spread with Python/Mesa
- A network agent based infection model with Mesa
- A simple agent based infection model with Mesa and Bokeh
mesa
- An individual based model of farm pathogen spread with Python/Mesa
- A network agent based infection model with Mesa
- A simple agent based infection model with Mesa and Bokeh
eurostat
immunology
jekyll
github
forestry
PySide2
tablexplore
linux
cso
- Ireland deaths in 2019/2020 compared to previous years
- Daily deaths in Ireland from RIP.ie in 2019 and 2020
- Visualizing Irish girls names since 1970
toytree
THOR
- Viewing the THOR dataset with Bokeh and Panel
- The scale of US bombing in Southeast Asia revealed in the THOR dataset
rip.ie
- Excess mortality in Ireland still high in 2023
- Excess mortality in Ireland is still high in 2022
- Ireland mortality data from RIP.ie, updated for 2021
- Deaths in Ireland from RIP.ie - another look
snipgenie
- 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
nanopore
phylogeny
ai
- 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.