Pinned Repositories
birch-beer
Generate a tree for displaying a hierarchy of groups with colors, scaling, and more.
fasta
The Fasta type as used by my programs.
find-clumpiness
Find the clumpiness of labels in a Haskell or JSON formatted tree.
heatitup
Find and annotate ITDs using suffix trees and characterize the exogenous segments within the spacer using heat diffusion.
hierarchical-spectral-clustering
Hierarchical spectral clustering of a graph.
multiomics-single-cell-t1d
Supplementary code for paper
ploterific
Basic plotting of tabular data for the command line.
spectral-clustering
Library for spectral clustering.
too-many-cells
Cluster single cells and analyze cell clade relationships with colorful visualizations.
tooManyCellsR
An R wrapper for too-many-cells, for clustering single cells and analyzing cell clade relationships with colorful visualizations.
GregorySchwartz's Repositories
GregorySchwartz/fasta
The Fasta type as used by my programs.
GregorySchwartz/find-clumpiness
Find the clumpiness of labels in a Haskell or JSON formatted tree.
GregorySchwartz/modify-fasta
Modify fasta (and CLIP) files in several ways.
GregorySchwartz/blosum
BLOSUM matrix generator with the addition of any generic characters for special amino acids
GregorySchwartz/convert-annotation
Convert the annotation of a gene to another in a delimited file using a variety of different databases.
GregorySchwartz/diversity
Calculates the diversity of each position in a fasta file.
GregorySchwartz/integreat
Integrate difference data sources and optionally perform differential integration.
GregorySchwartz/awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
GregorySchwartz/bedtools2
A powerful toolset for genome arithmetic.
GregorySchwartz/BiobaseNewick
GregorySchwartz/clumpiness
Library for measuring clumpiness of a hierarchical container such as a tree or dendrogram
GregorySchwartz/diagrams-builder
Utilities for creating diagram-building tools
GregorySchwartz/diagrams-graphviz
Graph layout and drawing with GraphViz and diagrams
GregorySchwartz/eigen
Haskell bindings to the Eigen C++ library
GregorySchwartz/ForestStructures
Tree and forest structures in Haskell
GregorySchwartz/github-orgmode-tests
This is a test project where you can explore how github interprets Org-mode files
GregorySchwartz/haskell-eigen
Haskel binding for Eigen library. Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
GregorySchwartz/hierarchical-clustering-diagrams
Draw diagrams of dendrograms made by hierarchical-clustering.
GregorySchwartz/hvega
Create Vega-Lite visualizations from Haskell.
GregorySchwartz/IHaskell
A Haskell kernel for IPython.
GregorySchwartz/normalize
normalize
GregorySchwartz/ox-latex-subfigure
Turn table into subfigure. More or less a hack atm, easy to incorporate to org-mode though
GregorySchwartz/palette
Tools for creating color schemes.
GregorySchwartz/random-tree
Library for creating random trees
GregorySchwartz/rank-product
Collects the functions pertaining to finding the rank product of a data set as well as the associated p-value.
GregorySchwartz/SciFlow
Scientific workflow management
GregorySchwartz/stackage
"Stable Hackage," tools for creating a vetted set of packages from Hackage.
GregorySchwartz/statistics
A fast, high quality library for computing with statistics in Haskell.
GregorySchwartz/subsample
Subsample data from a uniform distribution so two different statuses for the same entity have the same number of samples.
GregorySchwartz/tree-fun
Functions for tree exploration and manipulation