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adaptagrams

Libraries for constraint-based layout and connector routing for diagrams.

alphafold_singularity

Singularity recipe for AlphaFold

biocthis

Automate package and project setup for Bioconductor packages

bitutils

Core functions shared across multiple BioinfoTree commands

brusselator

The Brusselator, a mathematical model of a chemical oscillator

cabal-macosx

Haskell Cabal services for Mac OS X

cmph-cffi

Python bindings to the CMPH library

eurobioc2020

European Bioconductor Conference, December, 2020

gcng

R wrapper for GCNG

graphite

GRAPH Interaction from pathway Topological Environment

grisli

GRISLI: Gene Regulation Inference for Single-cell with LInear differential equations and Peanian kernel velocities

lace

Building SuperTranscripts: A linear representation of transcriptome data

messi

R wrapper for MESSI.

mitociaodata

Dataset of peptide spectrum matches for the Mitochondrial Complexes InterActome tOol (MitoCIAO)

network-theory

nichenetr

NicheNet: predict active ligand-target links between interacting cells

omicsdata

Support package for the "Omics Data" course

orna

Fast in-silico normalization algorithm for NGS data

parmigene

Parallel Mutual Information estimation for Gene Network reconstruction

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

scgco

R wrapper for scGCO

scvi-tools

Deep probabilistic analysis of single-cell omics data

seurat

R toolkit for single cell genomics

sir

Numerical solver for the SIR infection model by Kermack and McKendrick

spark

Spatially resolved transcriptomic analysis

spatialde

R wrapper for SpatialDE

stlearn

R wrapper for stLearn

transrate

Understand your transcriptome assembly

voyager

Benchmark for spatial expression

wikinetworks

WikiNetworks is a user-friendly Python package to process pathways from the WikiPathways database into machine-readable network representations.