15 projects
pegasuspy
Pegasus is a Python package for analyzing sc/snRNA-seq data of millions of cells
demuxEM
demuxEM is the demultiplexing module of Pegasus
pegasusio
Pegasusio is a Python package for reading / writing single-cell genomics data
harmony-pytorch
Pytorch implementation of Harmony algorithm on single-cell sequencing data integration
cirrocumulus
Bring your single-cell data to life
altocumulus
Command line utilities for workflows on Terra or Cromwell
stratocumulus
File backend component of Cumulus
nmf-torch
A PyTorch implementation on Non-negative Matrix Factorization.
forceatlas2-python
scRNA-Seq analysis tools that scale to millions of cells
sccloud
scRNA-Seq analysis tools that scale to millions of cells
MulticoreTSNE-modified
Forked from MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Fix a randomness error in tsne.cpp.
anndata-modified
Forked package from anndata v0.6.4, with a bug fix on reading string features. This fix was done following anndata official repository, but was not added to v0.6.4.
louvain-github
Forked from louvain-igraph (https://github.com/vtraag/louvain-igraph). Publish because its PyPI version is out-of-date, whereas our scCloud package depends on this github repo version. Will remove if a new release is published.
umap-learn-modified
Forked from umap-learn (https://github.com/lmcinnes/umap). Change API so that UMAP accepts precomputed KNN input, rather than always calculating by itself. Remove numba.njit parallel option to avoid delay in the cloud.
fisher-modified
Forked from fisher (https://github.com/brentp/fishers_exact_test). Recompile it with Cython 0.29.4 to be compatible with Python 3.7.
