Haskell Bioinformatics

Analyze, modify and simulate molecular sequence data and phylogenetic trees in a reproducible way.

Cluster single cells and analyze cell clade relationships with colorful visualizations.

Generate a tree for displaying a hierarchy of groups with colors, scaling, and more.

Finds out whether an entity comes from different distributions (statuses).

ABIF parser, writer and generator

Find and annotate ITDs with assembly or read pair joining using suffix trees and characterize the exogenous segments within the spacer using heat diffusion. A layer on top of heatitup for additional functionality such as working with BAM files directly.

Ensembl related functions and datastructures

Compile separate tex files with the same bibliography.

Hierarchical spectral clustering of a graph.

Haskell cabal libary for submission and result retrieval from the NCBI Entrez REST webservice

Process the output of heatitup in order to collapse sequences into clones by similar ITD mutations.

ViennaRNA v2 extensions in Haskell

Integrate difference data sources and optionally perform differential integration.

Find the modularity of a network.

normalize

Subsample data from a uniform distribution so two different statuses for the same entity have the same number of samples.

Automated theorem prover for a linear logic-based calculus for molecular biology.

Find and annotate ITDs.

merge two ordered Producers into a new Producer