Adam Gayoso's repositories
mplscience
Matplotlib style for scientific publications
bioconda-recipes
Conda recipes for the bioconda channel.
SingleCellOpenProblems
Formalizing and benchmarking open problems in single-cell genomics
anndata
Annotated data.
balanced-clustering
Reworked clustering metrics for assessing performance in imbalanced settings
biom-format
The Biological Observation Matrix (BIOM) Format Project
cell2location
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
conda-forge-pinning-feedstock
A conda-smithy repository for conda-forge-pinning.
cookiecutter-scverse
Cookiecutter template for scverse
jax
Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
scanpy
Single-Cell Analysis in Python. Scales to >1M cells.
scanpy-tutorials
Scanpy Tutorials.
scvelo
RNA Velocity generalized through dynamical modeling
scverse.github.io
scverse.org website
scVI
A deep generative model for gene expression profiles from single-cell RNA sequencing
scvi-tools-feedstock
A conda-smithy repository for scvi-tools.
seqc
Single-Cell Sequencing Quality Control and Processing Software
single-cell-studies
Example analysis using the 'Single cell studies database'
sphinx-automodapi
Sphinx extension for generating API documentation
staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
stereoscope
Spatial mapping of cell types by integration of transcriptomics data
umap
Uniform Manifold Approximation and Projection