Pinned Repositories
2023-June-Introduction-to-R-for-Bioinformatics
An introduction to the basic R programming for biologists. No data analysis experience necessary! Participants will gain skills necessary to run basic statistical analyses and generate figures in R.
abritamr
A pipeline for running AMRfinderPlus and collating results into functional classes
API_Hackathon
ApiBuilding
ApiRandom
ARGprofiler
A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
atlas
ATLAS - Three commands to start analyzing your metagenome data
carbon
:black_heart: Create and share beautiful images of your source code
gitworkshop
A repository for GitHub class
ilri-africa-cdc-training
A suite of pathogen genomics tutorials for the ILRI Genomics platform training programs
dkomics's Repositories
dkomics/ilri-africa-cdc-training
A suite of pathogen genomics tutorials for the ILRI Genomics platform training programs
dkomics/2023-June-Introduction-to-R-for-Bioinformatics
An introduction to the basic R programming for biologists. No data analysis experience necessary! Participants will gain skills necessary to run basic statistical analyses and generate figures in R.
dkomics/abritamr
A pipeline for running AMRfinderPlus and collating results into functional classes
dkomics/atlas
ATLAS - Three commands to start analyzing your metagenome data
dkomics/conda
OS-agnostic, system-level binary package manager and ecosystem
dkomics/FastMLST
⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies
dkomics/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
dkomics/fieldbioinformatics
The ARTIC field bioinformatics pipeline
dkomics/kcri-cge-bap
KCRI CGE Bacterial Analysis Pipeline
dkomics/medaka
Sequence correction provided by ONT Research
dkomics/MTBseq_source
MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
dkomics/transflow
A snakemake workflow for WGS-based tuberculosis transmission analysis
dkomics/ChemicalAssetTracker
The Chemical Asset Tracker is a web application that facilitates tracking and reporting on chemical inventories.
dkomics/Filtlong
quality filtering tool for long reads
dkomics/Git-and-GitHub-Masterclass---The-Practical-Bootcamp
Git an GitHub Masterclass - The Practical Bootcamp, by Packt Publishing
dkomics/kraken-protocol
Metagenome analysis using the Kraken software suite
dkomics/kraken2
The second version of the Kraken taxonomic sequence classification system
dkomics/mag
Assembly and binning of metagenomes
dkomics/miller
Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON
dkomics/miniforge
A conda-forge distribution.
dkomics/mmbdtp
Entry pages for course materials
dkomics/NanoPlot
Plotting scripts for long read sequencing data
dkomics/nextflow
A DSL for data-driven computational pipelines
dkomics/rgi
Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
dkomics/SeqSero2
SeqSero2
dkomics/snakemake-illumina-fastqc
A Snakemake workflow for quality control assessment of Illumina NGS data using FastQC and MultiQC
dkomics/snakemake_fa23
CCB Skills Seminar (Fall 2023) - snakemake
dkomics/training-material
A collection of Galaxy-related training material
dkomics/training_ONT_teaching
dkomics/web-portfolio