friedue

Chandran2021

Code and access to data related to the SIFT-seq publication by Chandran et al., Nature Medicine (2022)

GeartySchietinger

Scripts related to bulkRNA-seq as well as single-cell CITE-seq and VDJ-seq data of Gearty et al. (2021)

Scott2019

Code and data for the bulk RNA-seq and bulk ATAC-seq data of tumor-infiltrating CD8 T cells (and controls) as published in Scott et al., Nature (2019).

deepTools

Tools to process and analyze deep sequencing data.

course_RNA-seq2015

course_RNA-seq2017

course_RNA-seq2018

course_RNA-seq2019

Notes

Personal notes about work- and coding-related topics

SingleR

Clone of the Bioconductor repository for the SingleR package.

friedue/course_RNA-seq2019

friedue/Notes

Personal notes about work- and coding-related topics

friedue/course_RNA-seq2017

friedue/course_RNA-seq2018

friedue/Scott2019

Collection of scripts used for the analysis of high-throughput sequencing data (RNA-seq, ATAC-seq, ChIP-seq) for Scott et al., 2019.

friedue/spaeti

Functions for spatial transcriptomics (Visium)

friedue/Cancer_Epitopes_CSHL

A pipeline to approximate the immunogenicity of peptides resulting from cancer mutations based on structure and other factors.

friedue/celllabels

collection of cell labels from published single-cell omics data sets

friedue/CellTypeMIMB

friedue/DepLabData

clean some datasets

friedue/DittoSeq

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

friedue/djvdj

An R package to analyze AVID-seq data

friedue/DropletUtils

Clone of the Bioconductor repository for the DropletUtils package, see https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html for the official development version.

friedue/DRUID

A pipeline for reproducible transcriptome-wide measurements of mRNA stability

friedue/escape

Easy single cell analysis platform for enrichment

friedue/HIVSeqinR

Please download the latest version. "HIVSeqinR" is an R-based pipeline that processes HIV near-full-genome sequences and classifies genomes into "intact" or into various "defective" categories. Please see Wiki tab for more information.

friedue/lab-agile-planning

friedue/minion_qc

Quality control for MinION sequencing data

friedue/Proteomic_Correlation_Shiny

A Shiny App to Support Proteomic Correlation

friedue/randomScripts

collection of various scripts

friedue/Rd2mdMKDOCS

Package for creating markdown versions of R package reference manual.

friedue/Rmagic

friedue/SCEdjvdj

friedue/SingleR

A (history-edited) clone of https://github.com/dviraran/SingleR, in preparation for a Bioconductor submission.

friedue/SingleRBook-base

Contents to be compiled into the SingleR book.

friedue/snakecase

🐍🐍🐍 A systematic approach to parse strings and automate the conversion to snake_case, UpperCamelCase or any other case.

friedue/SNAPP

SNAPP sequencing data pipeline - haplotypes from targeted amplicon sequencing

friedue/STUtility

friedue/ThrivingInBioinformatics

friedue/wp2md

A script to convert Wordpress XML dump to markdown files