Pinned Repositories
endometriosis-scrnaseq
Code to reproduce analysis and figures for scRNA-seq analysis of endometriosis in Tan et al. 2021.
imc-preprocessor
Simple python app to quickly pre-process Imaging Mass Cytometry data for visualization and segmentation.
nf-tenx
All 10x Genomics processing pipelines rolled into one containerized pipelines
phenix-service
ventral-posterior-hypothalamus-scrnaseq
Code to reproduce analysis and figures for scRNA-seq analysis of the ventroposterior hypothalamus in Mickelsen et. al 2020
cbviz
Simple simulator for colorblindness
kronos-logout
A small script to automatically log you in and out of Kronos timekeeping systems.
multiseq-py
sc-marker-genes
Sets of marker genes used to identify cell types in scRNA-seq experiments
wflynny's Repositories
wflynny/sc-marker-genes
Sets of marker genes used to identify cell types in scRNA-seq experiments
wflynny/multiseq-py
wflynny/single-cell-methods
Meta repo linking single-cell RNA-seq tool aggregation repos
wflynny/biorxivfeed
Simple RSS feed reader and downloader for bioRxiv
wflynny/jax-vms
A few short setup scripts for VMs
wflynny/loupepy
Create a 10x Genomics Loupe file from an AnnData object
wflynny/cbviz
Simple simulator for colorblindness
wflynny/awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
wflynny/CITE-seq-Count
Small script that allows to count TAGS from a CITE-seq experiment
wflynny/gender-disparities
Gender disparities in science, funding, and more
wflynny/harmony
Scalable integration of single cell RNAseq data for batch correction and meta analysis
wflynny/inferCNV
Inferring CNV from Single-Cell RNA-Seq
wflynny/IntroToHPC
HPC and queue usage class syllabus
wflynny/JAX-NeuroGeneticsSClDataAnalysis
JAX: Neurogenetics Short Course Single cell data analysis
wflynny/JAX-Sleep-2023
wflynny/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
wflynny/keystone-single-cell-2019
Notes from the 2019 Keystone Symposium on Single Cell Biology
wflynny/MEDS6498-2019
Lecture notes on single cell genomics for MEDS6498-2019
wflynny/MEDS6498-2020
wflynny/pubs
Your bibliography on the command line
wflynny/python-novice-gapminder
Introduction to Python for non-programmers using gapminder data
wflynny/PythonImagingBasic
code and data for Basic Image Analysis in Python class
wflynny/sc-ngff
Musings on what a next-generation file format might look like for single cell 'omics and imaging
wflynny/sc-sifs
Singularity image files (.sif) for single cell genomic analyses
wflynny/scanpy_usage
Scanpy use cases.
wflynny/seqspec
machine-readable file format for genomic library sequence and structure
wflynny/seurat
R toolkit for single cell genomics
wflynny/solo
software to detect doublets
wflynny/tldr
:books: Simplified and community-driven man pages
wflynny/umap
Uniform Manifold Approximation and Projection