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scWGCNA
TODO: Link to the scWGCNA package
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Gene Distributions
TODO: Copy emmanuel’s notebook here
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Swan
TODO: Copy Fairlie’s notebook here
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Analysis of long-read transcriptomes
Author: Fairlie Reese Data download and formatting Long-read data Note: Astrocyte data currently not publically available. This page will be updated when it is! These files already contain full-length non-chimeric reads. They have been processed as per the pipeline outlined here # download files wget http://crick.bio.uci.edu/freese/210413_pgp1_hub/encode_files_dl.txt . xargs -L 1...
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Python on HPC3
Author: Emmanuel Dollinger How to run python on the HPC3 Sam Morabito recently showed me a trick to get python working on the HPC3. This makes running python on the HPC3 actually useable. This trick relies on using conda environments, you can read up on conda here and on conda...
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A Tale of Two Aligners
Author: Emmanuel Dollinger Introduction Goal of this notebook is to align mouse single cell transcriptomic reads using cellranger and kallisto to compare the outputs. All cellranger code was ran on the HPC3, all kallisto code was run on a desktop with 10 cores (which right there is a clue as...
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CellChat
GenPALS Seminar Presenter: Suoqin Jin Author of this page: Samuel Morabito Inference and analysis of cell-cell communication using CellChat Dr. Suoqin Jin gave a fantastic talk discussing CellChat, a tool for analyzing cell-cell commmunication using single-cell transcriptomics data. CellChat is a powerful analysis toolkit in R that allows for the...
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scVelo
Author: Sam Morabito Introduction In this tutorial, I will cover how to use the Python package scVelo to perform RNA velocity analysis in single-cell RNA-seq data (scRNA-seq). scVelo was published in 2020 in Nature Biotechnology, making several improvements from the original RNA velocity study and its accomanpying software velocyto. Briefly,...
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Scanorama
Author: Axel Almet introduction, installation, and data download Here, we will integrate four datasets of human pancreas cells from different studies. This collection has been used to benchmark a number of integration methods now and is used in the following Scanpy tutorial. It’s also worth mentioning that a lot of...