choener/overlay-bioinformatics

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Language
Nix
Created about 6 years ago
Updated over 1 year ago

choener/overlay-bioinformatics

choener

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nixos package overlays for bioinformatics tools

ADPfusion

Efficient, high-level dynamic programming

BiobaseXNA

efficient encoding of short RNA and DNA sequences

PrimitiveArray

no-frills Haskell arrays

FormalGrammars

Context-free and linear grammars in Haskell (parsing, pretty-printing, embedded DSL)

BiobaseInfernal

Haskell library to handle Infernal-related file formats

BiobaseFasta

streaming FASTA handling in Haskell

RNAfold

ViennaRNA RNAfold using the ADPfusion library

GenussFold

MCFGs for Genus-1 RNA Pseudoknots

BiobaseTypes

BiobaseBlast

BLAST-related tools

LinguisticsTypes

flake-rPackages

experimental flake to repackage rPackages

ForestStructures

Tree and forest structures in Haskell

SciBaseTypes

Base types and classes for statistics, sciences and humanities

OrderedBits

Order bits in a set by population count

GrammarProducts

Products of linear and context-free grammars

choener.github.io

Homepage Uni Jena

ADPfusionSet

dynamic programming for set data structures

DPutils

utilities for DP

WordAlignment

ViennaRNA-bindings

Bindings to the ViennaRNA package.

Forestry

Science and craft of forests

BiobaseTurner

Turner 2004 energy parameter parser

flowEMMi

automated model-based clustering of microbial data

ghcicabal

Provides a ghci shell with options parsed from multiple cabal files, simplifying work on multiple packages concurrently

BiobaseFR3D

Importer for FR3D resources

BenchmarkHistory

Simple Haskell benchmarking system with history

AlignmentAlgorithms

flake-aquadiva

Nix flake for aquadiva.uni-jena.de

Gene-CluEDO

Gene Cluster Evolution Determined Order

Discretized

Newtypes to generalize discretized floating point numbers

NaturalLanguageAlphabets

Alphabet and word encodings in natural languages

overlay-python-packages

overlay with python packages for nixos

ADPfusionForest

Dynamic programming on tree and forest structures

FeatureEngineering

Feature Engineering Examples

overlay-haskell-dev

haskell development related functionality

RNAdraw

overlay-haskell-packages

Overlay for modifications to existing Haskell packages (and potentially more)

Nussinov78

Nussinov78 using the ADPfusion library

BiobaseENA

European Nucleotide Archive data

flake-statistics

Flakes with a collection of statistical software

InternedData

Internization for (mostly string) data types

ViennaRNA-extras

ViennaRNA v2 extensions in Haskell

BiobaseVienna

RNAfold energy tables and Turner 2004 converter

CMCompare

Comparison of Infernal covariance models

bimaps

notmuch.nvim

Plugin to overlay email Message-IDs with the email subject. Requires notmuch.

ADPfusionSubword

BiobaseNewick