kalilamali
🧬👩🏻💻📊 Bioinformatician working on bacterial genomics at @SSI_dk
Statens Serum InstitutDenmark
Pinned Repositories
approval_tests_python_demo
This is a demo repo for testing in python using ApprovalTests.Python
codespaces-demo
This is a demo repo for CI and CD using GitHub codespaces and GitHub actions.
conda_ci_github_actions_demo
This is a demo repo for CI and CD for conda environments using GitHub actions.
Decision-support-in-dermatology
Scripts used in "Deep learning for decision support in dermatology". This work was presented as a M. Sc. Thesis for the Technical University of Denmark (DTU).
drawio_github_demo
This a demo repo for diagrams in GitHub using draw.io
Integrons
Integron analysis tools. Scripts necessary to reproduce the validation of IntFinder (version 1.0).
ISIC_2019_Machine_learning_for_Dermatology
This work was presented in a poster session as oral examination for DTU's course 02456 Deep learning.
SARS-CoV-2_Illumina_pipeline
Step-by-step approach in the analysis of SARS-CoV-2 cDNA from raw reads using fastqc, trimmomatic, bwa, vcftools.
skin_detector
Skin tone detector that uses the individual topology angle (ITA).
BPS_FBI_FSC_VirulenceFinder
Bash scripts to run virulencefinder and serotypefinder in local settings on ecoli fasta and fastq.gz files.
kalilamali's Repositories
kalilamali/skin_detector
Skin tone detector that uses the individual topology angle (ITA).
kalilamali/Decision-support-in-dermatology
Scripts used in "Deep learning for decision support in dermatology". This work was presented as a M. Sc. Thesis for the Technical University of Denmark (DTU).
kalilamali/bacteria_analyzer
Interactive program for handling data related to growth rates of different bacteria at different temperatures.
kalilamali/foodex2_code_meaning
An online or local app that takes an EFSA FoodEx2 code and returns its meaning.
kalilamali/ISIC_2019_Machine_learning_for_Dermatology
This work was presented in a poster session as oral examination for DTU's course 02456 Deep learning.
kalilamali/SARS-CoV-2_Illumina_pipeline
Step-by-step approach in the analysis of SARS-CoV-2 cDNA from raw reads using fastqc, trimmomatic, bwa, vcftools.
kalilamali/SKINdx
A local app that runs in your browser based on a deep learning system that can classify an image in 2 ways: Binary classification of skin vs. non-skin. 304 disease categories.
kalilamali/approval_tests_python_demo
This is a demo repo for testing in python using ApprovalTests.Python
kalilamali/atlassian_coursera_version_control_with_git
This is the final project for the atlassian coursera version control with git course.
kalilamali/bioweb_image_getter
This program gets Amphibia images from BIOWEB given a list with species names.
kalilamali/codespaces-demo
This is a demo repo for CI and CD using GitHub codespaces and GitHub actions.
kalilamali/conda_ci_github_actions_demo
This is a demo repo for CI and CD for conda environments using GitHub actions.
kalilamali/Dermatology
Machine learning experiments focus on skin lesions
kalilamali/drawio_github_demo
This a demo repo for diagrams in GitHub using draw.io
kalilamali/hugoforduke17
This is a sample hugo website for a duke Class
kalilamali/Integrons
Integron analysis tools. Scripts necessary to reproduce the validation of IntFinder (version 1.0).
kalilamali/duke_coursera_cloud_computing_foundations
This is the first lab for the duke coursera cloud computing foundations.
kalilamali/dukehugofeb1
this is a Hugo continuous delivery site
kalilamali/FishDNA_pipeline
Step-by-step approach in the analysis of Rainbow trout DNA from raw reads to population insights using fastqc, trimmomatic, bwa, vcftools, plink, and R.
kalilamali/Flask-Elastic-Beanstalk
kalilamali/gcp-flask-ml-deploy
This is a project to auto-deploy with an ML payload
kalilamali/github-actions-demo
This is a repo for building out Github Actions and Tricks
kalilamali/isic_2019
Skin lesion classifier for the ISIC 2019 challenge using Python and PyTorch.
kalilamali/kalilamali
kalilamali/kmodes_cluster_visualization
Get kmodes clusters from an excel sheet with data and visualize them as nested donut plots.
kalilamali/microbeseq_nbdev_augment
Files to assist in setup of nbdev
kalilamali/scaffold
This is a project scaffold for Python
kalilamali/simple-skin-detection
Skin tone estimation and segmentation in MATLAB and OpenCV
kalilamali/ucm_genomes_and_genome_analysis
R code in R Markdown used for ucm genomes and genome analysis course
kalilamali/Whole_genome_sequencing_analysis
Whole genome sequencing (WGS) was combined with bioinformatics tools to investigate the epidemiology of Vibrio cholerae in the Philippines and in other cholera affected countries.