RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

A document vector search with flexible matrix transforms. Currently supports Latent semantic analysis and Term frequency - inverse document frequency

A short tutorial on how to use RSEM

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tlock, RWMUTEX, Collab, USM, RSem and other C++ templates for Windows to provide read/write mutex locks, various multithreading tools, collaboration, differential updates and more

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

A shell pipeline for analyzing expression and variants in RNA-seq data based on STAR-RSEM and GATK

No description available

RSAM/RSEM - SSAM/SSEM easy code

An iOS component to present the email compose sheet with device and app info in the body

Simple preprocess + training script for GHA

STAR-RSEM pipeline for RNA-seq data processing

Contains TPM matrix (produced by RSEM) for pre-treatment samples from N = 42 ipilimumab-treated melanoma patients published in Van Allen et al. Science 2015.

STAR-RSEM pipeline in snakemake.

R package implementing parametric semicompeting risks in Stan

Workflows and more for RNA-seq data

Pipeline for low-level RNA-Seq data processing

Materials for the R Seminar

The RonR! Seminar Series are a series of seminars that were taught at Pompeu Fabra University in April-May 2016. This repository contains all the R scripts, presentations and exercises used for each separate session. Anyone interested in using these exercises go into each respective seminar and download the swirl exercises for themselves.

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R Seminar

This repo will be a project to learn, manage, and use the Yocto Project.

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Repository for UW Biology R Seminar Website

RNA-Seq Data Processing with STAR, RSEM, limma-voom

This is the pipeline used to perform the RSEM simulation based BLUEPRINT and Kolodziejczyk et al. benchmarks.

RNAseq workflow (RSEM, both classic and glm in EdgeR) for Melissa's thesis. Includes all downstream analyses (WGCNA, GO_MWU) and scripts to make figures (venn diagrams, heatmaps, word clouds).

RNA-seq pipeline in R/Bash enables QC, alignment, read counting, and differential expression using Bioconductor; reproducible workflow on Ubuntu with Conda. 🐙