erikrikarddaniel
I work with protein evolution and microbial ecology. Nowadays using mostly R/tidyverse, I have a long history in computing involving several tools.
Linnaeus University & Stockholm UniversityStockholm
Pinned Repositories
biomakefiles
Library makefiles for various bioinformatic tools.
eemisdada2
Packaging of dada2
environmentmicrobedb
A Ruby on Rails application for microbial diversity data from natural environments
gtdb-trees
hmmrank
Calculates a ranking of hmm profiles per sequence
magmap
Nextflow (nf-core) workflow for mapping reads to large collections of genomes.
pfitmap
pfitmap-db
Database construction tools for pfitmap-shiny
pfitmap-nextflow
Nextflow pipeline for hierarchical protein classification
taxdata2taxflat
Converts an NCBI taxonomy dump ("taxdata") to a flat tsv file with columns for recognized ranks.
erikrikarddaniel's Repositories
erikrikarddaniel/biomakefiles
Library makefiles for various bioinformatic tools.
erikrikarddaniel/gtdb-trees
erikrikarddaniel/magmap
Nextflow (nf-core) workflow for mapping reads to large collections of genomes.
erikrikarddaniel/hmmrank
Calculates a ranking of hmm profiles per sequence
erikrikarddaniel/pfitmap-db
Database construction tools for pfitmap-shiny
erikrikarddaniel/pfitmap-nextflow
Nextflow pipeline for hierarchical protein classification
erikrikarddaniel/3diphy
Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n for
erikrikarddaniel/ampliseq
16S rRNA amplicon sequencing analysis workflow using QIIME2
erikrikarddaniel/bioconda-recipes
Conda recipes for the bioconda channel.
erikrikarddaniel/dltemplates
Templates for various programming languages and tasks.
erikrikarddaniel/EUKulele
Automatic eukaryotic taxonomic classification
erikrikarddaniel/foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
erikrikarddaniel/funcscan
(Meta-)genome screening for functional and natural product gene sequences
erikrikarddaniel/gff2tsv
R script that converts gff files to tsv, splitting the attribute field into separate fields.
erikrikarddaniel/ki20240422
erikrikarddaniel/metatdenovo
erikrikarddaniel/nf-co.re
Code and files for the main nf-core website.
erikrikarddaniel/nf-core-ampliseq-symlink-bug
Repo for testing of potential symlink problem in Ampliseq
erikrikarddaniel/nf-core-mag
Assembly and binning of metagenomes
erikrikarddaniel/nf-core-magmap
erikrikarddaniel/nf-core-modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
erikrikarddaniel/nf-test
For Nextflow testing
erikrikarddaniel/phyloplace
erikrikarddaniel/pplaceeval
erikrikarddaniel/r4ds_seminars
R for data science seminar code and data
erikrikarddaniel/sativa
Semi-Automatic Taxonomy Improvement and Validation Algorithm
erikrikarddaniel/sbdi-phylomarkercheck
erikrikarddaniel/su-marine-microbiology
erikrikarddaniel/test-datasets
Test data to be used for automated testing with the nf-core pipelines
erikrikarddaniel/test_project