Bill Flynn's repositories
seqspec
machine-readable file format for genomic library sequence and structure
JAX-Sleep-AD-2022
Single Cell and Spatial Workshop, part of the Impacts of Sleep and Circadian Biology on Alzheimer’s Disease and Aging Short Course
gender-disparities
Gender disparities in science, funding, and more
sc-ngff
Musings on what a next-generation file format might look like for single cell 'omics and imaging
solo
software to detect doublets
sc-sifs
Singularity image files (.sif) for single cell genomic analyses
MEDS6498-2019
Lecture notes on single cell genomics for MEDS6498-2019
python-novice-gapminder
Introduction to Python for non-programmers using gapminder data
keystone-single-cell-2019
Notes from the 2019 Keystone Symposium on Single Cell Biology
PythonImagingBasic
code and data for Basic Image Analysis in Python class
harmony
Scalable integration of single cell RNAseq data for batch correction and meta analysis
tldr
:books: Simplified and community-driven man pages
sc-marker-genes
Sets of marker genes used to identify cell types in scRNA-seq experiments
seurat
R toolkit for single cell genomics
CITE-seq-Count
Small script that allows to count TAGS from a CITE-seq experiment
JAX-NeuroGeneticsSClDataAnalysis
JAX: Neurogenetics Short Course Single cell data analysis
awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
umap
Uniform Manifold Approximation and Projection
scanpy_usage
Scanpy use cases.
cbviz
Simple simulator for colorblindness
biorxivfeed
Simple RSS feed reader and downloader for bioRxiv
pubs
Your bibliography on the command line
inferCNV
Inferring CNV from Single-Cell RNA-Seq
IntroToHPC
HPC and queue usage class syllabus
single-cell-methods
Meta repo linking single-cell RNA-seq tool aggregation repos