Bill Flynn (wflynny)

wflynny

Geek Repo

Company:@TheJacksonLaboratory

Location:New Haven, CT, USA

Home Page:https://gist.github.com/wflynny

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Bill Flynn's repositories

sc-marker-genes

Sets of marker genes used to identify cell types in scRNA-seq experiments

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single-cell-methods

Meta repo linking single-cell RNA-seq tool aggregation repos

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biorxivfeed

Simple RSS feed reader and downloader for bioRxiv

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jax-vms

A few short setup scripts for VMs

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cbviz

Simple simulator for colorblindness

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awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

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CITE-seq-Count

Small script that allows to count TAGS from a CITE-seq experiment

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colorblindr

An R package to simulate colorblindness on R figures.

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gender-disparities

Gender disparities in science, funding, and more

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harmony

Scalable integration of single cell RNAseq data for batch correction and meta analysis

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inferCNV

Inferring CNV from Single-Cell RNA-Seq

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IntroToHPC

HPC and queue usage class syllabus

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JAX-NeuroGeneticsSClDataAnalysis

JAX: Neurogenetics Short Course Single cell data analysis

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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

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keystone-single-cell-2019

Notes from the 2019 Keystone Symposium on Single Cell Biology

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MEDS6498-2019

Lecture notes on single cell genomics for MEDS6498-2019

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pubs

Your bibliography on the command line

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python-novice-gapminder

Introduction to Python for non-programmers using gapminder data

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PythonImagingBasic

code and data for Basic Image Analysis in Python class

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sc-ngff

Musings on what a next-generation file format might look like for single cell 'omics and imaging

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sc-sifs

Singularity image files (.sif) for single cell genomic analyses

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scanpy_usage

Scanpy use cases.

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seqspec

machine-readable file format for genomic library sequence and structure

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seurat

R toolkit for single cell genomics

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solo

software to detect doublets

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tldr

:books: Simplified and community-driven man pages

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umap

Uniform Manifold Approximation and Projection

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