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allelespecific

pipeline for allele-specific mapping of short reads

bedtools

A powerful toolset for genome arithmetic.

cancer_epitopes_cshl

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

celllabels

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

celltypemimb

christmas

toy example for R packages

clustering

collection of scripts used for Chelmicki and Duendar et al. 2014

course_rna-seq2015

course_rna-seq2017

course_rna-seq2018

course_rna-seq2019

deplabdata

clean some datasets

dittoseq

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

djvdj

An R package to analyze AVID-seq data

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.

druid

A pipeline for reproducible transcriptome-wide measurements of mRNA stability

escape

Easy single cell analysis platform for enrichment

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.

lab-agile-planning

minion_qc

Quality control for MinION sequencing data

notes

Personal notes about work- and coding-related topics

phdthesis

proteomic_correlation_shiny

A Shiny App to Support Proteomic Correlation

randomscripts

collection of various scripts

rd2mdmkdocs

Package for creating markdown versions of R package reference manual.

rmagic

scedjvdj

scott2019

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

singler

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

singlerbook-base

Contents to be compiled into the SingleR book.