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awesome-single-cell

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

biorxivfeed

Simple RSS feed reader and downloader for bioRxiv

boinctoolkit

cbviz

Simple simulator for colorblindness

cellular_automaton

cellview

Simple App to visualize 10X single cell datasets

cite-seq-count

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

cluster-tools

colorblindr

An R package to simulate colorblindness on R figures.

flops-help

gender-disparities

Gender disparities in science, funding, and more

harmony

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

infercnv

Inferring CNV from Single-Cell RNA-Seq

introtohpc

HPC and queue usage class syllabus

jax-neurogeneticsscldataanalysis

JAX: Neurogenetics Short Course Single cell data analysis

jax-sleep-2023

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

jax-vms

A few short setup scripts for VMs

keystone-single-cell-2019

Notes from the 2019 Keystone Symposium on Single Cell Biology

kronos-logout

A small script to automatically log you in and out of Kronos timekeeping systems.

loupepy

Create a 10x Genomics Loupe file from an AnnData object

meds6498-2019

Lecture notes on single cell genomics for MEDS6498-2019

meds6498-2020

miseq-analysis

MiSeq analysis scripts for deep-sequencing project

multiseq-py

pdf-html-quickfix

Chrome extension to skip pesky "*pdf+html" pages when viewing journal articles

protease-couplings

Interactive visualizations of the interaction network of HIV protease residues

pubs

Your bibliography on the command line

python-novice-gapminder

Introduction to Python for non-programmers using gapminder data

pythonimagingbasic

code and data for Basic Image Analysis in Python class