Pinned Repositories
ADPfusion
Efficient, high-level dynamic programming
BiobaseBlast
BLAST-related tools
BiobaseFasta
streaming FASTA handling in Haskell
BiobaseInfernal
Haskell library to handle Infernal-related file formats
BiobaseTypes
BiobaseXNA
efficient encoding of short RNA and DNA sequences
flake-rPackages
experimental flake to repackage rPackages
FormalGrammars
Context-free and linear grammars in Haskell (parsing, pretty-printing, embedded DSL)
GenussFold
MCFGs for Genus-1 RNA Pseudoknots
PrimitiveArray
no-frills Haskell arrays
choener's Repositories
choener/ADPfusion
Efficient, high-level dynamic programming
choener/BiobaseXNA
efficient encoding of short RNA and DNA sequences
choener/FormalGrammars
Context-free and linear grammars in Haskell (parsing, pretty-printing, embedded DSL)
choener/BiobaseInfernal
Haskell library to handle Infernal-related file formats
choener/GenussFold
MCFGs for Genus-1 RNA Pseudoknots
choener/ForestStructures
Tree and forest structures in Haskell
choener/BiobaseTurner
Turner 2004 energy parameter parser
choener/choener.github.io
Homepage Uni Jena
choener/flowEMMi
automated model-based clustering of microbial data
choener/GrammarProducts
Products of linear and context-free grammars
choener/overlay-bioinformatics
nixos package overlays for bioinformatics tools
choener/SciBaseTypes
Base types and classes for statistics, sciences and humanities
choener/ViennaRNA-bindings
Bindings to the ViennaRNA package.
choener/ADPfusionSubword
choener/BiobaseENA
European Nucleotide Archive data
choener/BiobaseNewick
choener/flake-aquadiva
Nix flake for aquadiva.uni-jena.de
choener/ghcicabal
Provides a ghci shell with options parsed from multiple cabal files, simplifying work on multiple packages concurrently
choener/InternedData
Internization for (mostly string) data types
choener/notmuch.nvim
Plugin to overlay email Message-IDs with the email subject. Requires notmuch.
choener/ViennaRNA-extras
ViennaRNA v2 extensions in Haskell
choener/Chart-extras
Additional plot types for the Haskell chart library
choener/CompBio-Scripts
Selection of simple scripts for Computational Biology
choener/flake-ONT
Random ONT-related libraries packaped up as a flake
choener/KoboldAI-Client
choener/Online-MeanVar
Online calculation of mean and variance in Python
choener/Prj-GenussFold
Combined project for GenussFold via git subtree
choener/python-online-algorithms
Statistical online algorithms for Python.
choener/read5
Wrapper to read fast5, slow5, blow5 and pod5 files.
choener/RNAswarm
RNAswarm is a nextflow pipeline for differential RNA-RNA interaction analysis using RNA cross-linking methodologies