NEST-Interactive

CellNEST

TooManyCellsInteractive

TooManyPeaks

TooManyPeaks is an extension of TooManyCells for support with scATAC-seq data.

TooManyCells

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

modify-fasta

Modify fasta files in several ways.

inteGREAT

Integrate different data sources and optionally perform differential integration.

hierarchical-spectral-clustering

Hierarchical spectral clustering of a graph.

heatitup-complete

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.

fasta

A simple, mindless parser for fasta files.

diversity

Calculates the diversity of each position in a fasta file.

differential

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

convert-annotation

Convert the annotation of a gene to another in a delimited file using a variety of different databases.

clumpiness

Library for measuring clumpiness of a hierarchical container such as a tree or dendrogram.

birch-beer

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

heatitup

Find and annotate ITDs using suffix trees and characterize the exogenous segments within the spacer using heat diffusion.

find-clumpiness

Find the clumpiness of labels in a Haskell or JSON formatted tree.