Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by sirselim
A curated list of projects in awesome lists by sirselim .
https://github.com/sirselim/jetson_nanopore_sequencing
A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology.
Last synced: 07 Dec 2024
https://github.com/sirselim/guppy_parameter_optimiser
A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
basecalling gpu guppy nanopore-sequencing optimisation
Last synced: 08 Nov 2024
https://github.com/sirselim/illumina450k_filtering
A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays
bioinformatics methylation-analysis methylation-microarrays probes
Last synced: 07 Dec 2024
https://github.com/sirselim/diagnostics_exome_reporting
Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.
Last synced: 08 Nov 2024
https://github.com/sirselim/intro_to_gwas
An introductory workshop to GWAS analysis using PLINK and R
Last synced: 08 Nov 2024
https://github.com/sirselim/wes_shinydiscover
A Shiny interface to filter and identify variants of interest from whole exome data
Last synced: 18 Oct 2024
https://github.com/sirselim/methylation_ewas_workshop
This is a basic EWAS tutorial, introducing basic concepts for analysing methylation data
Last synced: 07 Dec 2024
https://github.com/sirselim/WES_ShinyDiscover
A Shiny interface to filter and identify variants of interest from whole exome data
Last synced: 16 Oct 2024
https://github.com/sirselim/electronic_lab_notebook
This is an example of using blogdown, hugo and netlify to create and serve an electronic lab notebook.
Last synced: 07 Dec 2024
https://github.com/sirselim/gpu-musings
A collection of my thoughts around GPUs for genomic analysis and sequencing
Last synced: 07 Dec 2024
https://github.com/sirselim/sirselim.github.io
Personal website, blog and notebook
Last synced: 07 Dec 2024
https://github.com/sirselim/vcf-dart_example_exomes
A few example exomes in vcf format for testing the VCF-DART annotation and reporting tool
Last synced: 07 Dec 2024
https://github.com/sirselim/tsne_plotting
some documentation for exploring the plotting of tSNE results from various data sources
Last synced: 07 Dec 2024
https://github.com/sirselim/presentation_and_design_resources
A small repo to hold useful resources for various courses I teach
Last synced: 07 Dec 2024
https://github.com/sirselim/cpg_annotate
small R script to provide quick annotation and gene lists for series of IlmnID's (450k probes)
Last synced: 07 Dec 2024
https://github.com/sirselim/vega-lite_integration_testing
A basic repository housing files detailing R and Python integration testing of vega-lite graphics
Last synced: 07 Dec 2024
https://github.com/sirselim/summary_metrics
A simple rust tool to generate statistics from ONT sequencing summary files
Last synced: 07 Dec 2024
https://github.com/sirselim/lyritical
Analysis of song and artist lyrics in R - just for fun!!
Last synced: 07 Dec 2024
https://github.com/sirselim/singularity-genmod
A quick singularity recipe for genmod to facilitate use in variant annotation pipelines
Last synced: 07 Dec 2024
https://github.com/sirselim/immunecell_methylation_paper_data
This repository contains data, results and supplementary information to go alongside our manuscript detailing the validation of immune cell specific methylation markers.
Last synced: 07 Dec 2024
https://github.com/sirselim/mtg-markdown-generator
A Python script to generate markdown tables for Magic: The Gathering cards using the Scryfall API.
Last synced: 07 Dec 2024
https://github.com/sirselim/mitofish
This script generates "baited" sequences from across a provided reference to search for them in fastq file(s)
Last synced: 07 Dec 2024
https://github.com/sirselim/presentation_learnings_from_ni
My presentation for the AGTA 2016 conference to be held in Auckland (Oct 9-12th, 2016)
Last synced: 07 Dec 2024
https://github.com/sirselim/r_notebooks
A quick overview of using R Notebooks as a form of electronic lab book for bioinformatics
Last synced: 07 Dec 2024
https://github.com/sirselim/nvidiagtc_2021
My 40min presentation for Nvidia Spring GTC 2021 on portable sequencing tech and Nvidia GPUs
nvidia nvidia-gpu nvidia-gtc presentation presentation-slides slide-deck slides
Last synced: 07 Dec 2024
https://github.com/sirselim/mtgcardfinder
MTG Card Markdown Toolkit - a VSCode extension to grab card image and information for markdown documents.
magic magic-the-gathering markdown mtg-cards
Last synced: 07 Dec 2024
https://github.com/sirselim/data_carpentry_notes
Notes made available for various data carpentry sessions
Last synced: 07 Dec 2024
https://github.com/sirselim/introduction-to-r-and-rstudio
An introductory overview of R and the fantastic IDE RStudio - rendered in Gitbook format
Last synced: 07 Dec 2024
https://github.com/sirselim/bookdown_lab_notebook
Testing bookdown as an electronic lab book option
Last synced: 07 Dec 2024
https://github.com/sirselim/clnr_401_plenary_presentation
My plenary presentation for the CLNR 401 weekend seminar
presentation presentation-slides
Last synced: 07 Dec 2024
https://github.com/sirselim/cmdhb-visit-jan2021
Short presention on portable sequencing for CMDHB visit to ESR
Last synced: 07 Dec 2024
https://github.com/sirselim/bedmeth2bedgraph
Small tool to convert bedmethyl format to custom bedgraph output
Last synced: 07 Dec 2024
https://github.com/sirselim/miles_cv
An online repository to provide an updated personal and professional CV.
Last synced: 07 Dec 2024
https://github.com/sirselim/frontline_genomics_presentation
Our presentation on 'real-time' genomics for ESR Data Science Week 2020.
base-calling genomics gpus nanopore-sequencing real-time
Last synced: 07 Dec 2024
https://github.com/sirselim/eresearch-presentation-2021
My eResearch 2021 presentation on portable sequencing technology and it's role in community driven science.
Last synced: 07 Dec 2024
https://github.com/sirselim/migraine_gene_lists
This repository curates and maintains a set of epilepsy 'related' genes in ranked tiers (biological priors)
Last synced: 07 Dec 2024
https://github.com/sirselim/powering_potential
a list of resources and information for the Powering Potential 2019 group working on "the which doctors" question (Human Genomics in NZ)
Last synced: 07 Dec 2024
https://github.com/sirselim/covid_analysis
Exploration of new Zealand COVID19 data from the MoH
Last synced: 07 Dec 2024
https://github.com/sirselim/presentation_maps
A repo to store maps used in my presentations
Last synced: 07 Dec 2024
https://github.com/sirselim/streamlit_app_test
A small repo to test out streamlit, a new tool for serving awesome web-based python apps.
Last synced: 07 Dec 2024
https://github.com/sirselim/sing_aotearoa_2018
Basic bioinformatics workshop for SING Aotearoa 2018 exploring population genetics and epigenetics
Last synced: 07 Dec 2024
https://github.com/sirselim/test_teams_link
A quick test to see if we can link GitHub content 'nicely' in MS Teams.
Last synced: 07 Dec 2024
https://github.com/sirselim/bootnet
bootNet is a wrapper for the fantastic glmnet function - it brings bootstrapping and parallel processing to the elastic-net framework.
Last synced: 07 Dec 2024
https://github.com/sirselim/alkresbaz_keystory_2020
My Key Story presentation for Auckland Research Bazaar 2020
genomics nanopore-sequencing sequencing
Last synced: 07 Dec 2024
https://github.com/sirselim/summary_simulator
A tool to quickly simulate some dummy Nanopore sequence summary data for testing purposes
Last synced: 07 Dec 2024
https://github.com/sirselim/random_plotting_scripts
A dump of some random and testing plotting scripts from various languages
Last synced: 07 Dec 2024
https://github.com/sirselim/wes_gene_lists
A curated list of genes used in the filtering steps of exome sequencing pipelines.
Last synced: 07 Dec 2024