crsky's repositories
pygna
A Python package for gene network analysis
epiScanpy
Episcanpy: Epigenomics Single Cell Analysis in Python
cellrank_reproducibility
CellRank's reproducibility repository.
scvi-tools-reproducibility
Reproducibility of results/figures from scvi-tools paper
MIRA
Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
Hands-On-Data-Analysis-with-Pandas-2nd-edition
Materials for following along with Hands-On Data Analysis with Pandas – Second Edition
handcalcs
Python library for converting Python calculations into rendered latex.
gwas-download
Easily download publicly available GWAS summary statistics.
python-ggseg
Python module for ggseg-like visualizations
MetBrewer
Color palette package in R inspired by works at the Metropolitan Museum of Art in New York
scvi-tools
Deep probabilistic analysis of single-cell omics data
geoCancerPrognosticDatasetsRetriever
GEO Cancer Prognostic Datasets Retriever is a bioinformatics tool for cancer prognostic dataset retrieval from the GEO website.
anndata
Annotated data.
dynamo-release
Inclusive model of expression dynamics with metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
OT-scOmics
This Jupyter Notebook will walk you trough the code to replicate the experiments from our research on applying Optimal Transport as a similarity metric in between single-cell omics data.
MultiVelo
Multi-omic velocity inference
pydata-book
Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media
leidenalg
Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
Scissor
Scissor package
mofax
Work with trained factor models in Python
scRNA-seq_notes
A list of scRNA-seq analysis tools
metaboss
The Metaplex NFT-standard Swiss Army Knife tool.
datawizard
Magic potions to clean and transform your data 🧙
TieDIE
Tied Diffusion for Subnetwork Discovery (TieDIE)
liger
R package for integrating and analyzing multiple single-cell datasets
scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
skylab
Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
Seurat-to-RNA-Velocity
A guide to using a Seurat object in conjunction with RNA Velocity
r-color-palettes
Comprehensive list of color palettes available in R ❤️🧡💛💚💙💜