mikelove

awesome-multi-omics

List of software packages for multi-omics analysis

preNivolumabOnNivolumab

EDA, QC, and DESeq2 / edgeR analysis of 109 RNA-seq samples of immunotherapy treatment

alpine

Modeling and correcting fragment sequence bias for RNA-seq

mrlocus

Older repo for MRLocus. See new website for software usage guide:

plyrangesTximetaCaseStudy

A case study for the combination of plyranges and tximeta Bioconductor packages

ase-sim

mikelove.github.io

Love Lab website

plyrangesMLmisc

miscellaneous ideas of plyranges implementations or extensions

test_pydeseq2

igvf_spdi_demo

larsson-2021

osteoblast-quant

PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

s4demo

Minimal demo of a simple S4 method and class setup

ads2020

Advanced Data Science 2020 Edition

Bioc2022AllelicExpression

Bioc2022 workshop. SEESAW: Statistical Estimation Of Allelic Expression Using Salmon And Swish

BioC2023

bioconductor.org

Website for bioconductor.org

boot-basics

cd4-overlaps

checkfiles

ensembldb

This is the ensembldb development repository.

igvfR

R/Shiny demo accessing data via IGVF Catalog API

pkgrevdocs

Training Material for Community Reviewers

plotgardener

plyranges

A grammar of genomic data transformation

stageR

stageR package

swish-ase-assessment

tidybulk

Brings bulk and pseudobulk transcriptomics to the tidyverse

tidySummarizedExperiment

Brings SummarizedExperiment to the tidyverse