Ben Johnson's repositories
compartmap
Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq
biscuit
BISulfite-seq CUI Toolkit
biscuiteer
tools for analysing Biscuit (https://huishenlab.github.io/biscuit/) output
compartmap_manuscript
This repository contains all the code and much of the processed data for the compartmap manuscript
datasets
Datasets related to the IGVF workflows
how_are_we_stranded_here
Check strandedness of RNA-Seq fastq files
kallisto
Near-optimal RNA-Seq quantification
kb_python
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
myfirstrepo
This is for VAIGS 2021 bioinformatics course git session
ngs-tools
Reusable tools for working with next-generation sequencing (NGS) data
QDNAseq_bin_annotations
This repo contains bin annotations for QDNAseq CNA calling
sleuth
Differential analysis of RNA-Seq
stormseq_protocols
This repository contains the current STORM-seq protocol for library construction and analysis
synthbar
Add synthetic cell barcode to FASTQ reads
TCGA_TGCT_metharray_analysis
This repository contains public analysis scripts for processing and producing figures for the TCGA TGCT cohort
velocessor
velocity processor
WGBS_Biscuit_Snakemake
Snakemake Workflow For WGBS Data
wzmetagene
Create sub-intervals from intervals